Thu Sep 26 18:01:31 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all -s BIO-ALS-701-088-BL -i /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-088-BL/anat/BIO-ALS-701-088-BL_T1w.nii.gz -all -brainstem-structures -qcache -3T subjid BIO-ALS-701-088-BL setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 65535 memorylocked 64 kbytes maxproc 1030094 maxlocks unlimited maxsignal 1030094 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 263890112 5406252 246813800 96744 11670060 257339964 Swap: 65535996 0 65535996 ######################################## 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: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.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: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:31-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.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: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.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: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/09/26-22:01:32-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: mn457 Machine: aura.nmr.mgh.harvard.edu Platform: Linux PlatformVersion: 3.10.0-957.1.3.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_convert /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-088-BL/anat/BIO-ALS-701-088-BL_T1w.nii.gz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-088-BL/anat/BIO-ALS-701-088-BL_T1w.nii.gz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/Data/BIOMARKER/BIO-ALS-701-088-BL/anat/BIO-ALS-701-088-BL_T1w.nii.gz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99863, 5.2336e-18, 0.052336) j_ras = (0, 1, -1e-16) k_ras = (-0.052336, 0, 0.99863) writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Thu Sep 26 18:01:41 EDT 2019 Found 1 runs /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig/001.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_convert /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz --conform mri_convert.bin /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99863, 5.2336e-18, 0.052336) j_ras = (0, 1, -1e-16) k_ras = (-0.052336, 0, 0.99863) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz... mri_add_xform_to_header -c /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/talairach.xfm /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Sep 26 18:01:58 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 26 18:01:58 EDT 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.46758 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.46758/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.46758/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, -6.61744e-24) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.46758/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 26 18:02:01 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.46758/nu0.mnc ./tmp.mri_nu_correct.mni.46758/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.46758/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mn457@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/] [2019-09-26 18:02:01] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/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 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.46758/0/ ./tmp.mri_nu_correct.mni.46758/nu0.mnc ./tmp.mri_nu_correct.mni.46758/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Number of iterations: 54 CV of field change: 0.000952395 [mn457@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/] [2019-09-26 18:03:14] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.46758/nu0.mnc ./tmp.mri_nu_correct.mni.46758/0//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.46758/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.46758/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.46758/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, -6.61744e-24) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Thu Sep 26 18:03:28 EDT 2019 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Thu Sep 26 18:03:29 EDT 2019 Ended at Thu Sep 26 18:04:03 EDT 2019 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Sep 26 18:04:05 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3562, pval=0.0406 >= threshold=0.0050) awk -f /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/extract_talairach_avi_QA.awk /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/talairach_avi.log TalAviQA: 0.97233 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Thu Sep 26 18:04:05 EDT 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Thu Sep 26 18:04:05 EDT 2019 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.3187 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3187/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.3187/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, -6.61744e-24) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.3187/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Sep 26 18:04:09 EDT 2019 nu_correct -clobber ./tmp.mri_nu_correct.mni.3187/nu0.mnc ./tmp.mri_nu_correct.mni.3187/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3187/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [mn457@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/] [2019-09-26 18:04:09] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/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 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.3187/0/ ./tmp.mri_nu_correct.mni.3187/nu0.mnc ./tmp.mri_nu_correct.mni.3187/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Use of ?PATTERN? without explicit operator is deprecated at /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/sharpen_volume line 153. Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Number of iterations: 54 CV of field change: 0.000952395 [mn457@aura.nmr.mgh.harvard.edu:/autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/] [2019-09-26 18:05:22] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.3187/nu0.mnc ./tmp.mri_nu_correct.mni.3187/0//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.3187/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3187/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.3187/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.3187/ones.mgz sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 input ./tmp.mri_nu_correct.mni.3187/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.3187/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.3187/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3187/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3187/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.3187/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.3187/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3187/input.mean.dat sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3187/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.3187/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.3187/ones.mgz --i ./tmp.mri_nu_correct.mni.3187/nu1.mnc --sum ./tmp.mri_nu_correct.mni.3187/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3187/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.3187/ones.mgz --i ./tmp.mri_nu_correct.mni.3187/nu1.mnc --sum ./tmp.mri_nu_correct.mni.3187/sum.junk --avgwf ./tmp.mri_nu_correct.mni.3187/output.mean.dat sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 Loading ./tmp.mri_nu_correct.mni.3187/ones.mgz Loading ./tmp.mri_nu_correct.mni.3187/nu1.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.3187/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.3187/nu1.mnc ./tmp.mri_nu_correct.mni.3187/nu1.mnc mul .88622338459979053812 Saving result to './tmp.mri_nu_correct.mni.3187/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.3187/nu1.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.3187/nu1.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.3187/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, -6.61744e-24) 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 8 seconds. mapping (26, 149) to ( 3, 110) Thu Sep 26 18:06:14 EDT 2019 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Thu Sep 26 18:06:15 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 1.04535 -0.03807 0.09261 0.99541; 0.01263 0.82471 0.47750 -9.91438; -0.10645 -0.42764 0.93638 12.02884; 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 = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 75 (75), valley at 49 (49) csf peak at 23, setting threshold to 57 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 75 (75), valley at 46 (46) csf peak at 22, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 41 seconds. #-------------------------------------------- #@# Skull Stripping Thu Sep 26 18:07:57 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_em_register -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_withskull_2016-05-10.vc700.gca'... average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=14.0 skull bounding box = (45, 49, 10) --> (207, 255, 233) using (99, 118, 122) as brain centroid... mean wm in atlas = 108, using box (79,93,94) --> (118, 143,149) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 108 +- 5.9 after smoothing, mri peak at 108, scaling input intensities by 1.000 scaling channel 0 by 1 initial log_p = -4.505 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.396142 @ (-9.091, -9.091, -9.091) max log p = -4.376564 @ (4.545, -4.545, 4.545) max log p = -4.291069 @ (2.273, 2.273, -2.273) max log p = -4.280049 @ (1.136, -1.136, -1.136) max log p = -4.280049 @ (0.000, 0.000, 0.000) max log p = -4.274426 @ (-0.852, 0.284, -0.284) Found translation: (-2.0, -12.2, -8.2): log p = -4.274 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.032, old_max_log_p =-4.274 (thresh=-4.3) 1.05465 0.11036 0.04825 -31.71053; -0.15011 0.90627 0.39622 -25.91632; 0.00000 -0.33145 0.85472 60.24586; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.018, old_max_log_p =-4.032 (thresh=-4.0) 1.06505 -0.00221 -0.01800 -7.75501; -0.01063 0.92702 0.54435 -56.96601; 0.02106 -0.48042 0.85537 80.49686; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.010, old_max_log_p =-4.018 (thresh=-4.0) 1.05421 0.12596 0.03803 -31.87262; -0.15219 0.97368 0.42674 -32.32407; 0.01949 -0.35531 0.91910 54.76414; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.010, old_max_log_p =-4.010 (thresh=-4.0) 1.05421 0.12596 0.03803 -31.87262; -0.15219 0.97368 0.42674 -32.32407; 0.01949 -0.35531 0.91910 54.76414; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.932, old_max_log_p =-4.010 (thresh=-4.0) 1.02887 0.15512 0.05348 -32.89859; -0.19065 0.97928 0.50264 -37.06345; 0.02883 -0.41010 0.87192 63.34492; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.929, old_max_log_p =-3.932 (thresh=-3.9) 1.01971 0.08821 0.02196 -18.21201; -0.12147 0.98144 0.46740 -43.70837; 0.02258 -0.37784 0.88790 59.38091; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.898, old_max_log_p =-3.929 (thresh=-3.9) 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.898, old_max_log_p =-3.898 (thresh=-3.9) 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.898 (old=-4.505) transform before final EM align: 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 012: -log(p) = 4.3 tol 0.000000 final transform: 1.02090 0.08831 0.02198 -19.31828; -0.12170 0.98175 0.47633 -44.77256; 0.02354 -0.38538 0.88302 60.49079; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... mri_em_register utimesec 1523.787612 mri_em_register stimesec 5.685341 mri_em_register ru_maxrss 609780 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1078700 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 24 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 22 mri_em_register ru_nivcsw 414 registration took 25 minutes and 30 seconds. mri_watershed -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mri_watershed.dat -T1 -brain_atlas /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=123 z=111 r=87 first estimation of the main basin volume: 2807349 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=112, y=113, z=70, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=9724481062 voxels, voxel volume =1.000 = 9724481062 mmm3 = 9724481.536 cm3 done. PostAnalyze...Basin Prior 84 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=133, z=106, r=10560 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=33 , nb = 43354 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = -1027937203 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=63 , nb = -1056750292 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = -1094325316 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=29 , nb = 1068862812 OTHER CSF_MIN=3, CSF_intensity=26, CSF_MAX=38 , nb = 1081042334 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 33, 39, 45, 72 after analyzing : 33, 43, 45, 50 RIGHT_CER before analyzing : 56, 47, 42, 78 after analyzing : 35, 47, 47, 54 LEFT_CER before analyzing : 63, 47, 38, 75 after analyzing : 35, 47, 47, 54 RIGHT_BRAIN before analyzing : 29, 36, 44, 73 after analyzing : 29, 41, 44, 49 LEFT_BRAIN before analyzing : 29, 37, 45, 72 after analyzing : 29, 42, 45, 49 OTHER before analyzing : 38, 6, 0, 2 after analyzing : 6, 18, 25, 19 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.010 curvature mean = 73.896, std = 7.690 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.64, sigma = 11.15 after rotation: sse = 5.64, sigma = 11.15 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 9.27, its var is 19.52 before Erosion-Dilatation 9.07% of inacurate vertices after Erosion-Dilatation 12.92% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1969684 voxels, voxel volume = 1.000 mm3 = 1969684 mmm3 = 1969.684 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 21.318004 mri_watershed stimesec 0.586862 mri_watershed ru_maxrss 834124 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 398734 mri_watershed ru_majflt 0 mri_watershed ru_nswap 0 mri_watershed ru_inblock 0 mri_watershed ru_oublock 3112 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 88 mri_watershed ru_nivcsw 14 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Sep 26 18:33:50 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_em_register -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 = 1 == reading 1 input volumes... logging results to talairach.log reading '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.9 skull bounding box = (59, 66, 25) --> (194, 211, 199) using (104, 114, 112) as brain centroid... mean wm in atlas = 107, using box (87,96,91) --> (120, 131,133) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 6.2 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.183 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.094223 @ (-9.091, -9.091, 9.091) max log p = -4.033221 @ (4.545, -4.545, -13.636) max log p = -3.980400 @ (2.273, 6.818, 2.273) max log p = -3.968101 @ (-1.136, -1.136, -1.136) max log p = -3.961626 @ (1.705, -0.568, 0.568) max log p = -3.945333 @ (-0.284, 0.284, -0.284) Found translation: (-2.0, -8.2, -3.1): log p = -3.945 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.945 (thresh=-3.9) 0.99144 0.12059 0.04995 -21.68917; -0.14032 0.98467 0.40787 -40.00354; 0.00000 -0.35398 0.85459 57.80510; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.559, old_max_log_p =-3.559 (thresh=-3.6) 0.99144 0.12059 0.04995 -21.68917; -0.14032 0.98467 0.40787 -40.00354; 0.00000 -0.35398 0.85459 57.80510; 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=-3.386, old_max_log_p =-3.559 (thresh=-3.6) 0.99144 0.12059 0.04995 -21.68917; -0.13510 0.94980 0.38852 -30.35123; 0.00067 -0.36499 0.86778 59.76290; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.386, old_max_log_p =-3.386 (thresh=-3.4) 0.99144 0.12059 0.04995 -21.68917; -0.13510 0.94980 0.38852 -30.35123; 0.00067 -0.36499 0.86778 59.76290; 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=-3.367, old_max_log_p =-3.386 (thresh=-3.4) 0.99548 0.09244 0.07122 -21.73427; -0.11905 0.94118 0.41890 -33.61680; -0.02744 -0.40101 0.85551 70.37402; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.360, old_max_log_p =-3.367 (thresh=-3.4) 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.360, old_max_log_p =-3.360 (thresh=-3.4) 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.360 (old=-4.183) transform before final EM align: 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 3.9 tol 0.000000 final transform: 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 1081.861619 mri_em_register stimesec 4.001551 mri_em_register ru_maxrss 602972 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 919841 mri_em_register ru_majflt 0 mri_em_register ru_nswap 0 mri_em_register ru_inblock 0 mri_em_register ru_oublock 32 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 38 mri_em_register ru_nivcsw 295 registration took 18 minutes and 6 seconds. #-------------------------------------- #@# CA Normalize Thu Sep 26 18:51:56 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=26.9 skull bounding box = (59, 66, 25) --> (194, 211, 199) using (104, 114, 112) as brain centroid... mean wm in atlas = 107, using box (87,96,91) --> (120, 131,133) to find MRI wm before smoothing, mri peak at 108 robust fit to distribution - 107 +- 6.2 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246344 sample points... INFO: compute sample coordinates transform 0.99528 0.08338 0.05024 -17.34078; -0.10262 0.94157 0.41929 -35.83387; -0.01115 -0.39944 0.85657 67.01196; 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, 66, 31) --> (196, 192, 201) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 1872 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 64, 30) --> (132, 180, 200) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 1 of 2091 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 161, 70) --> (173, 205, 125) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 16 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 160, 64) --> (126, 200, 124) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 11 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (107, 141, 100) --> (143, 208, 134) Brain_Stem: limiting intensities to 91.0 --> 132.0 0 of 50 (0.0%) samples deleted using 4040 total control points for intensity normalization... bias field = 0.983 +- 0.047 36 of 4039 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 66, 31) --> (196, 192, 201) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 2250 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 64, 30) --> (132, 180, 200) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 2473 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 161, 70) --> (173, 205, 125) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 13 of 76 (17.1%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 160, 64) --> (126, 200, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 5 of 77 (6.5%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (107, 141, 100) --> (143, 208, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 20 of 99 (20.2%) samples deleted using 4975 total control points for intensity normalization... bias field = 1.027 +- 0.047 21 of 4906 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 66, 31) --> (196, 192, 201) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 0 of 2277 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (62, 64, 30) --> (132, 180, 200) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 132.0 1 of 2507 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (126, 161, 70) --> (173, 205, 125) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 22 of 88 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (79, 160, 64) --> (126, 200, 124) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 41 of 86 (47.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (107, 141, 100) --> (143, 208, 134) Brain_Stem: limiting intensities to 88.0 --> 132.0 105 of 251 (41.8%) samples deleted using 5209 total control points for intensity normalization... bias field = 1.023 +- 0.046 15 of 4969 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 14 seconds. #-------------------------------------- #@# CA Reg Thu Sep 26 18:53:10 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_ca_register -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 0.98 (predicted orig area = 8.2) 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=0.814, neg=0, invalid=762 0001: dt=238.151240, rms=0.757 (6.927%), neg=0, invalid=762 0002: dt=221.952000, rms=0.746 (1.513%), neg=0, invalid=762 0003: dt=221.952000, rms=0.739 (0.872%), neg=0, invalid=762 0004: dt=169.000000, rms=0.735 (0.574%), neg=0, invalid=762 0005: dt=369.920000, rms=0.731 (0.541%), neg=0, invalid=762 0006: dt=129.472000, rms=0.728 (0.468%), neg=0, invalid=762 0007: dt=517.888000, rms=0.724 (0.553%), neg=0, invalid=762 0008: dt=129.472000, rms=0.721 (0.330%), neg=0, invalid=762 0009: dt=517.888000, rms=0.718 (0.382%), neg=0, invalid=762 0010: dt=129.472000, rms=0.717 (0.224%), neg=0, invalid=762 0011: dt=129.472000, rms=0.716 (0.094%), neg=0, invalid=762 0012: dt=129.472000, rms=0.715 (0.139%), neg=0, invalid=762 0013: dt=129.472000, rms=0.714 (0.203%), neg=0, invalid=762 0014: dt=129.472000, rms=0.712 (0.225%), neg=0, invalid=762 0015: dt=129.472000, rms=0.711 (0.217%), neg=0, invalid=762 0016: dt=129.472000, rms=0.709 (0.204%), neg=0, invalid=762 0017: dt=129.472000, rms=0.708 (0.152%), neg=0, invalid=762 0018: dt=129.472000, rms=0.707 (0.127%), neg=0, invalid=762 0019: dt=129.472000, rms=0.706 (0.125%), neg=0, invalid=762 0020: dt=129.472000, rms=0.706 (0.102%), neg=0, invalid=762 0021: dt=221.952000, rms=0.705 (0.015%), neg=0, invalid=762 0022: dt=221.952000, rms=0.705 (0.071%), neg=0, invalid=762 0023: dt=221.952000, rms=0.704 (0.070%), neg=0, invalid=762 0024: dt=221.952000, rms=0.704 (0.044%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.705, neg=0, invalid=762 0025: dt=129.472000, rms=0.703 (0.276%), neg=0, invalid=762 0026: dt=517.888000, rms=0.701 (0.199%), neg=0, invalid=762 0027: dt=517.888000, rms=0.700 (0.182%), neg=0, invalid=762 0028: dt=517.888000, rms=0.700 (0.076%), neg=0, invalid=762 0029: dt=517.888000, rms=0.699 (0.094%), neg=0, invalid=762 0030: dt=517.888000, rms=0.699 (-0.195%), neg=0, invalid=762 0031: dt=129.472000, rms=0.697 (0.236%), neg=0, invalid=762 0032: dt=517.888000, rms=0.696 (0.110%), neg=0, invalid=762 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.701, neg=0, invalid=762 0033: dt=93.161290, rms=0.696 (0.667%), neg=0, invalid=762 0034: dt=251.259259, rms=0.686 (1.535%), neg=0, invalid=762 0035: dt=47.515152, rms=0.682 (0.601%), neg=0, invalid=762 0036: dt=580.608000, rms=0.671 (1.489%), neg=0, invalid=762 0037: dt=75.650873, rms=0.665 (0.989%), neg=0, invalid=762 0038: dt=25.920000, rms=0.664 (0.058%), neg=0, invalid=762 0039: dt=25.920000, rms=0.664 (0.022%), neg=0, invalid=762 0040: dt=25.920000, rms=0.664 (0.018%), neg=0, invalid=762 0041: dt=25.920000, rms=0.664 (0.044%), neg=0, invalid=762 0042: dt=25.920000, rms=0.663 (0.121%), neg=0, invalid=762 0043: dt=25.920000, rms=0.662 (0.196%), neg=0, invalid=762 0044: dt=25.920000, rms=0.660 (0.221%), neg=0, invalid=762 0045: dt=25.920000, rms=0.659 (0.210%), neg=0, invalid=762 0046: dt=25.920000, rms=0.658 (0.203%), neg=0, invalid=762 0047: dt=25.920000, rms=0.656 (0.190%), neg=0, invalid=762 0048: dt=25.920000, rms=0.655 (0.162%), neg=0, invalid=762 0049: dt=25.920000, rms=0.654 (0.173%), neg=0, invalid=762 0050: dt=25.920000, rms=0.653 (0.198%), neg=0, invalid=762 0051: dt=25.920000, rms=0.651 (0.210%), neg=0, invalid=762 0052: dt=25.920000, rms=0.650 (0.197%), neg=0, invalid=762 0053: dt=25.920000, rms=0.649 (0.187%), neg=0, invalid=762 0054: dt=25.920000, rms=0.648 (0.160%), neg=0, invalid=762 0055: dt=25.920000, rms=0.647 (0.139%), neg=0, invalid=762 0056: dt=25.920000, rms=0.646 (0.120%), neg=0, invalid=762 0057: dt=25.920000, rms=0.645 (0.131%), neg=0, invalid=762 0058: dt=25.920000, rms=0.645 (0.130%), neg=0, invalid=762 0059: dt=25.920000, rms=0.644 (0.131%), neg=0, invalid=762 0060: dt=25.920000, rms=0.643 (0.107%), neg=0, invalid=762 0061: dt=25.920000, rms=0.642 (0.095%), neg=0, invalid=762 0062: dt=0.025312, rms=0.642 (0.001%), neg=0, invalid=762 0063: dt=0.025312, rms=0.642 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.643, neg=0, invalid=762 0064: dt=97.361702, rms=0.640 (0.406%), neg=0, invalid=762 0065: dt=36.288000, rms=0.640 (0.061%), neg=0, invalid=762 0066: dt=36.288000, rms=0.640 (0.034%), neg=0, invalid=762 0067: dt=36.288000, rms=0.640 (0.054%), neg=0, invalid=762 0068: dt=36.288000, rms=0.639 (0.039%), neg=0, invalid=762 0069: dt=36.288000, rms=0.639 (0.030%), neg=0, invalid=762 0070: dt=124.416000, rms=0.639 (0.023%), neg=0, invalid=762 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=762 0071: dt=11.200000, rms=0.662 (0.272%), neg=0, invalid=762 0072: dt=9.600000, rms=0.662 (0.045%), neg=0, invalid=762 0073: dt=9.600000, rms=0.662 (0.019%), neg=0, invalid=762 0074: dt=9.600000, rms=0.661 (-0.054%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.662, neg=0, invalid=762 0075: dt=4.800000, rms=0.661 (0.119%), neg=0, invalid=762 0076: dt=2.400000, rms=0.661 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.713, neg=0, invalid=762 0077: dt=6.266667, rms=0.701 (1.642%), neg=0, invalid=762 0078: dt=5.583333, rms=0.700 (0.198%), neg=0, invalid=762 0079: dt=5.583333, rms=0.700 (0.005%), neg=0, invalid=762 0080: dt=5.583333, rms=0.700 (-0.202%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.700, neg=0, invalid=762 0081: dt=0.000000, rms=0.700 (0.095%), neg=0, invalid=762 0082: dt=0.000000, rms=0.700 (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=0.742, neg=0, invalid=762 0083: dt=0.000000, rms=0.741 (0.085%), neg=0, invalid=762 0084: dt=0.000000, rms=0.741 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.742, neg=0, invalid=762 0085: dt=0.000000, rms=0.741 (0.085%), neg=0, invalid=762 0086: dt=0.000000, rms=0.741 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.671, neg=0, invalid=762 0087: dt=0.806068, rms=0.654 (2.583%), neg=0, invalid=762 0088: dt=0.064000, rms=0.653 (0.109%), neg=0, invalid=762 0089: dt=0.064000, rms=0.653 (-0.042%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.654, neg=0, invalid=762 0090: dt=0.028000, rms=0.653 (0.128%), neg=0, invalid=762 0091: dt=0.007000, rms=0.653 (0.002%), neg=0, invalid=762 0092: dt=0.007000, rms=0.653 (-0.001%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.13454 (18) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1876 voxels, overlap=0.634) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (1876 voxels, peak = 17), gca=17.3 gca peak = 0.15565 (16) mri peak = 0.12532 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1792 voxels, overlap=0.818) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (1792 voxels, peak = 17), gca=16.6 gca peak = 0.26829 (96) mri peak = 0.06920 (95) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1037 voxels, overlap=1.008) Right_Pallidum (52): linear fit = 0.99 x + 0.0 (1037 voxels, peak = 95), gca=94.6 gca peak = 0.20183 (93) mri peak = 0.08045 (100) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (963 voxels, overlap=0.444) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (963 voxels, peak = 99), gca=99.0 gca peak = 0.21683 (55) mri peak = 0.07613 (70) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1136 voxels, overlap=0.020) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (1136 voxels, peak = 66), gca=66.3 gca peak = 0.30730 (58) mri peak = 0.07651 (75) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (755 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.26 x + 0.0 (755 voxels, peak = 73), gca=73.4 gca peak = 0.11430 (101) mri peak = 0.13803 (105) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (82560 voxels, overlap=0.619) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (82560 voxels, peak = 105), gca=104.5 gca peak = 0.12076 (102) mri peak = 0.12483 (105) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (85242 voxels, overlap=0.656) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (85242 voxels, peak = 105), gca=104.5 gca peak = 0.14995 (59) mri peak = 0.03338 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (29562 voxels, overlap=0.012) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (29562 voxels, peak = 73), gca=73.5 gca peak = 0.15082 (58) mri peak = 0.03872 (75) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (31496 voxels, overlap=0.001) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (31496 voxels, peak = 75), gca=75.1 gca peak = 0.14161 (67) mri peak = 0.11069 (81) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1056 voxels, overlap=0.105) Right_Caudate (50): linear fit = 1.20 x + 0.0 (1056 voxels, peak = 80), gca=80.1 gca peak = 0.15243 (71) mri peak = 0.10947 (83) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1272 voxels, overlap=0.348) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1272 voxels, peak = 78), gca=78.5 gca peak = 0.13336 (57) mri peak = 0.03205 (62) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (30169 voxels, overlap=0.849) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (30169 voxels, peak = 64), gca=63.6 gca peak = 0.13252 (56) mri peak = 0.03216 (62) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (34641 voxels, overlap=0.555) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (34641 voxels, peak = 69), gca=69.2 gca peak = 0.18181 (84) mri peak = 0.07332 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11397 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (11397 voxels, peak = 89), gca=89.5 gca peak = 0.20573 (83) mri peak = 0.08609 (87) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (10133 voxels, overlap=0.806) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (10133 voxels, peak = 88), gca=87.6 gca peak = 0.21969 (57) mri peak = 0.08132 (78) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (402 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (402 voxels, peak = 76), gca=75.5 gca peak = 0.39313 (56) mri peak = 0.08744 (73) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (586 voxels, overlap=0.028) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (586 voxels, peak = 71), gca=71.4 gca peak = 0.14181 (85) mri peak = 0.05569 (94) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (6708 voxels, overlap=0.764) Left_Thalamus_Proper (10): linear fit = 1.09 x + 0.0 (6708 voxels, peak = 92), gca=92.2 gca peak = 0.11978 (83) mri peak = 0.08303 (84) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5734 voxels, overlap=0.851) Right_Thalamus_Proper (49): linear fit = 1.01 x + 0.0 (5734 voxels, peak = 84), gca=84.2 gca peak = 0.13399 (79) mri peak = 0.05919 (84) Left_Putamen (12): linear fit = 1.14 x + 0.0 (3027 voxels, overlap=0.494) Left_Putamen (12): linear fit = 1.14 x + 0.0 (3027 voxels, peak = 90), gca=90.5 gca peak = 0.14159 (79) mri peak = 0.08378 (88) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2960 voxels, overlap=0.452) Right_Putamen (51): linear fit = 1.10 x + 0.0 (2960 voxels, peak = 87), gca=86.5 gca peak = 0.10025 (80) mri peak = 0.09337 (87) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14966 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (14966 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.09688 (89) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1456 voxels, overlap=0.663) Right_VentralDC (60): linear fit = 1.03 x + 0.0 (1456 voxels, peak = 89), gca=89.0 gca peak = 0.12801 (89) mri peak = 0.09759 (93) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1593 voxels, overlap=0.621) Left_VentralDC (28): linear fit = 1.07 x + 0.0 (1593 voxels, peak = 95), gca=94.8 gca peak = 0.20494 (23) mri peak = 0.22222 (21) gca peak = 0.15061 (21) mri peak = 0.10209 (18) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (519 voxels, overlap=0.858) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (519 voxels, peak = 23), gca=22.8 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 1.27 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=762 0093: dt=89.459178, rms=0.626 (2.233%), neg=0, invalid=762 0094: dt=129.472000, rms=0.625 (0.248%), neg=0, invalid=762 0095: dt=369.920000, rms=0.623 (0.280%), neg=0, invalid=762 0096: dt=221.952000, rms=0.622 (0.104%), neg=0, invalid=762 0097: dt=295.936000, rms=0.621 (0.168%), neg=0, invalid=762 0098: dt=92.480000, rms=0.621 (0.080%), neg=0, invalid=762 0099: dt=369.920000, rms=0.620 (0.055%), neg=0, invalid=762 0100: dt=129.472000, rms=0.620 (0.110%), neg=0, invalid=762 0101: dt=129.472000, rms=0.619 (0.027%), neg=0, invalid=762 0102: dt=129.472000, rms=0.619 (0.045%), neg=0, invalid=762 0103: dt=129.472000, rms=0.619 (0.059%), neg=0, invalid=762 0104: dt=129.472000, rms=0.618 (0.080%), neg=0, invalid=762 0105: dt=129.472000, rms=0.618 (0.087%), neg=0, invalid=762 0106: dt=129.472000, rms=0.617 (0.092%), neg=0, invalid=762 0107: dt=129.472000, rms=0.617 (0.095%), neg=0, invalid=762 0108: dt=129.472000, rms=0.616 (0.102%), neg=0, invalid=762 0109: dt=129.472000, rms=0.615 (0.093%), neg=0, invalid=762 0110: dt=129.472000, rms=0.615 (0.079%), neg=0, invalid=762 0111: dt=129.472000, rms=0.614 (0.070%), neg=0, invalid=762 0112: dt=129.472000, rms=0.614 (0.073%), neg=0, invalid=762 0113: dt=129.472000, rms=0.614 (0.080%), neg=0, invalid=762 0114: dt=129.472000, rms=0.613 (0.091%), neg=0, invalid=762 0115: dt=129.472000, rms=0.612 (0.087%), neg=0, invalid=762 0116: dt=129.472000, rms=0.612 (0.067%), neg=0, invalid=762 0117: dt=129.472000, rms=0.612 (0.060%), neg=0, invalid=762 0118: dt=129.472000, rms=0.611 (0.056%), neg=0, invalid=762 0119: dt=129.472000, rms=0.611 (0.048%), neg=0, invalid=762 0120: dt=129.472000, rms=0.611 (0.057%), neg=0, invalid=762 0121: dt=129.472000, rms=0.610 (0.058%), neg=0, invalid=762 0122: dt=129.472000, rms=0.610 (0.060%), neg=0, invalid=762 0123: dt=129.472000, rms=0.610 (0.048%), neg=0, invalid=762 0124: dt=129.472000, rms=0.609 (0.049%), neg=0, invalid=762 0125: dt=129.472000, rms=0.609 (0.042%), neg=0, invalid=762 0126: dt=129.472000, rms=0.609 (0.038%), neg=0, invalid=762 0127: dt=129.472000, rms=0.609 (0.053%), neg=0, invalid=762 0128: dt=129.472000, rms=0.608 (0.049%), neg=0, invalid=762 0129: dt=129.472000, rms=0.608 (0.049%), neg=0, invalid=762 0130: dt=129.472000, rms=0.608 (0.033%), neg=0, invalid=762 0131: dt=129.472000, rms=0.608 (0.030%), neg=0, invalid=762 0132: dt=129.472000, rms=0.607 (0.027%), neg=0, invalid=762 0133: dt=129.472000, rms=0.607 (0.036%), neg=0, invalid=762 0134: dt=129.472000, rms=0.607 (0.044%), neg=0, invalid=762 0135: dt=129.472000, rms=0.607 (0.041%), neg=0, invalid=762 0136: dt=129.472000, rms=0.606 (0.027%), neg=0, invalid=762 0137: dt=129.472000, rms=0.606 (0.020%), neg=0, invalid=762 0138: dt=129.472000, rms=0.606 (0.022%), neg=0, invalid=762 0139: dt=129.472000, rms=0.606 (0.022%), neg=0, invalid=762 0140: dt=517.888000, rms=0.606 (0.037%), neg=0, invalid=762 0141: dt=0.000000, rms=0.606 (0.001%), neg=0, invalid=762 0142: dt=0.850000, rms=0.606 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.606, neg=0, invalid=762 0143: dt=369.920000, rms=0.604 (0.308%), neg=0, invalid=762 0144: dt=129.472000, rms=0.604 (0.064%), neg=0, invalid=762 0145: dt=443.904000, rms=0.604 (0.031%), neg=0, invalid=762 0146: dt=443.904000, rms=0.604 (0.003%), neg=0, invalid=762 0147: dt=443.904000, rms=0.604 (-0.450%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.605, neg=0, invalid=762 0148: dt=36.288000, rms=0.603 (0.268%), neg=0, invalid=762 0149: dt=145.152000, rms=0.601 (0.304%), neg=0, invalid=762 0150: dt=145.152000, rms=0.596 (0.845%), neg=0, invalid=762 0151: dt=36.288000, rms=0.595 (0.137%), neg=0, invalid=762 0152: dt=248.832000, rms=0.593 (0.399%), neg=0, invalid=762 0153: dt=96.196319, rms=0.590 (0.486%), neg=0, invalid=762 0154: dt=36.288000, rms=0.589 (0.142%), neg=0, invalid=762 0155: dt=331.776000, rms=0.587 (0.336%), neg=0, invalid=762 0156: dt=75.004525, rms=0.585 (0.421%), neg=0, invalid=762 0157: dt=62.208000, rms=0.584 (0.100%), neg=0, invalid=762 0158: dt=331.776000, rms=0.583 (0.280%), neg=0, invalid=762 0159: dt=36.288000, rms=0.581 (0.225%), neg=0, invalid=762 0160: dt=145.152000, rms=0.581 (0.133%), neg=0, invalid=762 0161: dt=82.944000, rms=0.580 (0.151%), neg=0, invalid=762 0162: dt=82.944000, rms=0.579 (0.079%), neg=0, invalid=762 0163: dt=124.416000, rms=0.578 (0.147%), neg=0, invalid=762 0164: dt=36.288000, rms=0.578 (0.070%), neg=0, invalid=762 0165: dt=497.664000, rms=0.577 (0.241%), neg=0, invalid=762 0166: dt=36.288000, rms=0.575 (0.269%), neg=0, invalid=762 0167: dt=145.152000, rms=0.574 (0.157%), neg=0, invalid=762 0168: dt=36.288000, rms=0.574 (0.045%), neg=0, invalid=762 0169: dt=36.288000, rms=0.574 (0.027%), neg=0, invalid=762 0170: dt=36.288000, rms=0.573 (0.049%), neg=0, invalid=762 0171: dt=36.288000, rms=0.573 (0.070%), neg=0, invalid=762 0172: dt=36.288000, rms=0.572 (0.099%), neg=0, invalid=762 0173: dt=36.288000, rms=0.572 (0.120%), neg=0, invalid=762 0174: dt=36.288000, rms=0.571 (0.128%), neg=0, invalid=762 0175: dt=36.288000, rms=0.570 (0.136%), neg=0, invalid=762 0176: dt=36.288000, rms=0.569 (0.138%), neg=0, invalid=762 0177: dt=36.288000, rms=0.569 (0.138%), neg=0, invalid=762 0178: dt=36.288000, rms=0.568 (0.136%), neg=0, invalid=762 0179: dt=36.288000, rms=0.567 (0.132%), neg=0, invalid=762 0180: dt=36.288000, rms=0.566 (0.129%), neg=0, invalid=762 0181: dt=36.288000, rms=0.566 (0.132%), neg=0, invalid=762 0182: dt=36.288000, rms=0.565 (0.133%), neg=0, invalid=762 0183: dt=36.288000, rms=0.564 (0.123%), neg=0, invalid=762 0184: dt=36.288000, rms=0.564 (0.121%), neg=0, invalid=762 0185: dt=36.288000, rms=0.563 (0.113%), neg=0, invalid=762 0186: dt=36.288000, rms=0.562 (0.100%), neg=0, invalid=762 0187: dt=36.288000, rms=0.562 (0.094%), neg=0, invalid=762 0188: dt=36.288000, rms=0.561 (0.095%), neg=0, invalid=762 0189: dt=36.288000, rms=0.561 (0.096%), neg=0, invalid=762 0190: dt=36.288000, rms=0.560 (0.092%), neg=0, invalid=762 0191: dt=36.288000, rms=0.560 (0.096%), neg=0, invalid=762 0192: dt=36.288000, rms=0.559 (0.093%), neg=0, invalid=762 0193: dt=36.288000, rms=0.559 (0.085%), neg=0, invalid=762 0194: dt=36.288000, rms=0.558 (0.083%), neg=0, invalid=762 0195: dt=36.288000, rms=0.558 (0.075%), neg=0, invalid=762 0196: dt=36.288000, rms=0.557 (0.067%), neg=0, invalid=762 0197: dt=36.288000, rms=0.557 (0.069%), neg=0, invalid=762 0198: dt=36.288000, rms=0.557 (0.076%), neg=0, invalid=762 0199: dt=36.288000, rms=0.556 (0.070%), neg=0, invalid=762 0200: dt=36.288000, rms=0.556 (0.071%), neg=0, invalid=762 0201: dt=36.288000, rms=0.555 (0.062%), neg=0, invalid=762 0202: dt=36.288000, rms=0.555 (0.068%), neg=0, invalid=762 0203: dt=36.288000, rms=0.555 (0.060%), neg=0, invalid=762 0204: dt=36.288000, rms=0.554 (0.058%), neg=0, invalid=762 0205: dt=36.288000, rms=0.554 (0.060%), neg=0, invalid=762 0206: dt=36.288000, rms=0.554 (0.060%), neg=0, invalid=762 0207: dt=36.288000, rms=0.553 (0.056%), neg=0, invalid=762 0208: dt=36.288000, rms=0.553 (0.053%), neg=0, invalid=762 0209: dt=36.288000, rms=0.553 (0.056%), neg=0, invalid=762 0210: dt=36.288000, rms=0.553 (0.054%), neg=0, invalid=762 0211: dt=36.288000, rms=0.552 (0.051%), neg=0, invalid=762 0212: dt=36.288000, rms=0.552 (0.048%), neg=0, invalid=762 0213: dt=36.288000, rms=0.552 (0.047%), neg=0, invalid=762 0214: dt=36.288000, rms=0.552 (0.048%), neg=0, invalid=762 0215: dt=36.288000, rms=0.551 (0.046%), neg=0, invalid=762 0216: dt=36.288000, rms=0.551 (0.045%), neg=0, invalid=762 0217: dt=36.288000, rms=0.551 (0.040%), neg=0, invalid=762 0218: dt=36.288000, rms=0.551 (0.005%), neg=0, invalid=762 0219: dt=36.288000, rms=0.551 (0.004%), neg=0, invalid=762 0220: dt=9.072000, rms=0.551 (0.003%), neg=0, invalid=762 0221: dt=2.268000, rms=0.551 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.551, neg=0, invalid=762 0222: dt=145.152000, rms=0.549 (0.467%), neg=0, invalid=762 0223: dt=36.288000, rms=0.548 (0.069%), neg=0, invalid=762 0224: dt=124.416000, rms=0.548 (0.064%), neg=0, invalid=762 0225: dt=124.416000, rms=0.547 (0.080%), neg=0, invalid=762 0226: dt=62.208000, rms=0.547 (0.050%), neg=0, invalid=762 0227: dt=248.832000, rms=0.547 (0.071%), neg=0, invalid=762 0228: dt=36.288000, rms=0.546 (0.052%), neg=0, invalid=762 0229: dt=331.776000, rms=0.546 (0.067%), neg=0, invalid=762 0230: dt=36.288000, rms=0.546 (0.050%), neg=0, invalid=762 0231: dt=82.944000, rms=0.546 (0.022%), neg=0, invalid=762 0232: dt=82.944000, rms=0.546 (0.018%), neg=0, invalid=762 0233: dt=82.944000, rms=0.545 (0.031%), neg=0, invalid=762 0234: dt=82.944000, rms=0.545 (0.061%), neg=0, invalid=762 0235: dt=82.944000, rms=0.545 (0.061%), neg=0, invalid=762 0236: dt=82.944000, rms=0.544 (0.057%), neg=0, invalid=762 0237: dt=82.944000, rms=0.544 (0.064%), neg=0, invalid=762 0238: dt=82.944000, rms=0.544 (0.081%), neg=0, invalid=762 0239: dt=82.944000, rms=0.543 (0.069%), neg=0, invalid=762 0240: dt=82.944000, rms=0.543 (0.066%), neg=0, invalid=762 0241: dt=82.944000, rms=0.543 (0.045%), neg=0, invalid=762 0242: dt=82.944000, rms=0.542 (0.074%), neg=0, invalid=762 0243: dt=82.944000, rms=0.542 (0.054%), neg=0, invalid=762 0244: dt=82.944000, rms=0.542 (0.059%), neg=0, invalid=762 0245: dt=82.944000, rms=0.541 (0.029%), neg=0, invalid=762 0246: dt=82.944000, rms=0.541 (0.062%), neg=0, invalid=762 0247: dt=82.944000, rms=0.541 (0.044%), neg=0, invalid=762 0248: dt=82.944000, rms=0.541 (0.054%), neg=0, invalid=762 0249: dt=82.944000, rms=0.540 (0.033%), neg=0, invalid=762 0250: dt=82.944000, rms=0.540 (0.076%), neg=0, invalid=762 0251: dt=82.944000, rms=0.540 (0.027%), neg=0, invalid=762 0252: dt=82.944000, rms=0.540 (0.054%), neg=0, invalid=762 0253: dt=82.944000, rms=0.540 (0.014%), neg=0, invalid=762 0254: dt=82.944000, rms=0.539 (0.076%), neg=0, invalid=762 0255: dt=82.944000, rms=0.539 (0.032%), neg=0, invalid=762 0256: dt=82.944000, rms=0.539 (0.070%), neg=0, invalid=762 0257: dt=82.944000, rms=0.539 (0.006%), neg=0, invalid=762 0258: dt=82.944000, rms=0.538 (0.076%), neg=0, invalid=762 0259: dt=82.944000, rms=0.538 (0.047%), neg=0, invalid=762 0260: dt=82.944000, rms=0.538 (0.063%), neg=0, invalid=762 0261: dt=82.944000, rms=0.537 (0.039%), neg=0, invalid=762 0262: dt=82.944000, rms=0.537 (0.037%), neg=0, invalid=762 0263: dt=82.944000, rms=0.537 (0.029%), neg=0, invalid=762 0264: dt=82.944000, rms=0.537 (0.041%), neg=0, invalid=762 0265: dt=82.944000, rms=0.537 (0.044%), neg=0, invalid=762 0266: dt=82.944000, rms=0.536 (0.036%), neg=0, invalid=762 0267: dt=82.944000, rms=0.536 (0.029%), neg=0, invalid=762 0268: dt=82.944000, rms=0.536 (0.018%), neg=0, invalid=762 0269: dt=82.944000, rms=0.536 (0.037%), neg=0, invalid=762 0270: dt=82.944000, rms=0.536 (0.034%), neg=0, invalid=762 0271: dt=82.944000, rms=0.535 (0.041%), neg=0, invalid=762 0272: dt=82.944000, rms=0.535 (0.023%), neg=0, invalid=762 0273: dt=82.944000, rms=0.535 (0.015%), neg=0, invalid=762 0274: dt=82.944000, rms=0.535 (0.026%), neg=0, invalid=762 0275: dt=31.104000, rms=0.535 (0.001%), neg=0, invalid=762 0276: dt=31.104000, rms=0.535 (0.002%), neg=0, invalid=762 0277: dt=31.104000, rms=0.535 (-0.002%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.543, neg=0, invalid=762 0278: dt=19.200000, rms=0.542 (0.180%), neg=0, invalid=762 0279: dt=44.800000, rms=0.541 (0.158%), neg=0, invalid=762 0280: dt=153.600000, rms=0.537 (0.710%), neg=0, invalid=762 0281: dt=32.000000, rms=0.536 (0.205%), neg=0, invalid=762 0282: dt=128.000000, rms=0.532 (0.666%), neg=0, invalid=762 0283: dt=11.200000, rms=0.531 (0.179%), neg=0, invalid=762 0284: dt=2.800000, rms=0.531 (0.041%), neg=0, invalid=762 0285: dt=1.400000, rms=0.531 (0.013%), neg=0, invalid=762 0286: dt=0.700000, rms=0.531 (0.005%), neg=0, invalid=762 0287: dt=0.175000, rms=0.531 (0.002%), neg=0, invalid=762 0288: dt=0.043750, rms=0.531 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=762 0289: dt=58.236025, rms=0.527 (0.713%), neg=0, invalid=762 0290: dt=32.000000, rms=0.526 (0.296%), neg=0, invalid=762 0291: dt=44.800000, rms=0.525 (0.155%), neg=0, invalid=762 0292: dt=38.400000, rms=0.524 (0.197%), neg=0, invalid=762 0293: dt=32.000000, rms=0.523 (0.117%), neg=0, invalid=762 0294: dt=11.200000, rms=0.523 (0.087%), neg=0, invalid=762 0295: dt=38.400000, rms=0.522 (0.138%), neg=0, invalid=762 0296: dt=102.400000, rms=0.521 (0.150%), neg=0, invalid=762 0297: dt=11.200000, rms=0.521 (0.115%), neg=0, invalid=762 0298: dt=9.600000, rms=0.520 (0.071%), neg=0, invalid=762 0299: dt=0.700000, rms=0.520 (0.005%), neg=0, invalid=762 0300: dt=0.350000, rms=0.520 (0.001%), neg=0, invalid=762 0301: dt=0.010937, rms=0.520 (-0.001%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0302: dt=1.000000, rms=0.534 (0.081%), neg=0, invalid=762 0303: dt=0.252000, rms=0.534 (0.002%), neg=0, invalid=762 0304: dt=0.252000, rms=0.534 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.534, neg=0, invalid=762 0305: dt=1.008000, rms=0.534 (0.082%), neg=0, invalid=762 0306: dt=0.864000, rms=0.534 (0.004%), neg=0, invalid=762 0307: dt=0.864000, rms=0.534 (-0.003%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.560, neg=0, invalid=762 0308: dt=1.792000, rms=0.557 (0.547%), neg=0, invalid=762 0309: dt=0.448000, rms=0.557 (0.021%), neg=0, invalid=762 0310: dt=0.448000, rms=0.557 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.557, neg=0, invalid=762 0311: dt=1.792000, rms=0.555 (0.342%), neg=0, invalid=762 0312: dt=1.280000, rms=0.555 (0.047%), neg=0, invalid=762 0313: dt=1.280000, rms=0.555 (-0.011%), 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=0.530, neg=0, invalid=762 0314: dt=0.448000, rms=0.515 (2.824%), neg=0, invalid=762 0315: dt=1.280000, rms=0.506 (1.904%), neg=0, invalid=762 0316: dt=0.000000, rms=0.506 (-0.001%), neg=0, invalid=762 0317: dt=0.050000, rms=0.506 (-0.017%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=762 0318: dt=0.448000, rms=0.502 (0.819%), neg=0, invalid=762 0319: dt=0.448000, rms=0.501 (0.100%), neg=0, invalid=762 0320: dt=0.448000, rms=0.501 (0.102%), neg=0, invalid=762 0321: dt=0.448000, rms=0.501 (0.062%), neg=0, invalid=762 0322: dt=0.448000, rms=0.500 (0.055%), neg=0, invalid=762 0323: dt=0.448000, rms=0.500 (0.039%), neg=0, invalid=762 0324: dt=0.448000, rms=0.500 (0.040%), neg=0, invalid=762 0325: dt=0.448000, rms=0.500 (0.065%), neg=0, invalid=762 0326: dt=0.448000, rms=0.499 (0.080%), neg=0, invalid=762 0327: dt=0.448000, rms=0.499 (0.090%), neg=0, invalid=762 0328: dt=0.448000, rms=0.498 (0.086%), neg=0, invalid=762 0329: dt=0.448000, rms=0.498 (0.074%), neg=0, invalid=762 0330: dt=0.448000, rms=0.498 (0.058%), neg=0, invalid=762 0331: dt=0.448000, rms=0.497 (0.041%), neg=0, invalid=762 0332: dt=0.448000, rms=0.497 (0.025%), neg=0, invalid=762 0333: dt=0.448000, rms=0.497 (0.009%), neg=0, invalid=762 0334: dt=0.448000, rms=0.497 (-0.007%), neg=0, invalid=762 0335: dt=0.000000, rms=0.497 (0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0336: dt=0.000000, rms=0.495 (0.083%), neg=0, invalid=762 0337: dt=0.000000, rms=0.495 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0338: dt=110.976000, rms=0.495 (0.092%), neg=0, invalid=762 0339: dt=443.904000, rms=0.495 (0.034%), neg=0, invalid=762 0340: dt=443.904000, rms=0.495 (-0.452%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0341: dt=9.072000, rms=0.495 (0.094%), neg=0, invalid=762 0342: dt=6.480000, rms=0.495 (0.002%), neg=0, invalid=762 0343: dt=6.480000, rms=0.495 (0.000%), neg=0, invalid=762 0344: dt=6.480000, rms=0.495 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=762 0345: dt=145.152000, rms=0.493 (0.413%), neg=0, invalid=762 0346: dt=36.288000, rms=0.493 (0.098%), neg=0, invalid=762 0347: dt=36.288000, rms=0.492 (0.052%), neg=0, invalid=762 0348: dt=36.288000, rms=0.492 (0.079%), neg=0, invalid=762 0349: dt=36.288000, rms=0.492 (0.098%), neg=0, invalid=762 0350: dt=36.288000, rms=0.491 (0.119%), neg=0, invalid=762 0351: dt=36.288000, rms=0.490 (0.122%), neg=0, invalid=762 0352: dt=36.288000, rms=0.490 (0.117%), neg=0, invalid=762 0353: dt=36.288000, rms=0.489 (0.101%), neg=0, invalid=762 0354: dt=103.680000, rms=0.489 (0.033%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.490, neg=0, invalid=762 0355: dt=37.046595, rms=0.487 (0.646%), neg=0, invalid=762 0356: dt=44.800000, rms=0.484 (0.509%), neg=0, invalid=762 0357: dt=25.600000, rms=0.482 (0.388%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0358: dt=44.800000, rms=0.481 (0.266%), neg=0, invalid=762 0359: dt=25.600000, rms=0.480 (0.240%), neg=0, invalid=762 0360: dt=25.600000, rms=0.479 (0.083%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0361: dt=25.600000, rms=0.478 (0.233%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0362: dt=25.600000, rms=0.477 (0.286%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 11 iterations, nbhd size=1, neg = 0 0363: dt=25.600000, rms=0.476 (0.194%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 2 iterations, nbhd size=0, neg = 0 0364: dt=25.600000, rms=0.475 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0365: dt=25.600000, rms=0.474 (0.235%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 5 iterations, nbhd size=0, neg = 0 0366: dt=25.600000, rms=0.473 (0.229%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0367: dt=25.600000, rms=0.473 (0.134%), neg=0, invalid=762 iter 0, gcam->neg = 8 after 4 iterations, nbhd size=0, neg = 0 0368: dt=25.600000, rms=0.472 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 10 after 11 iterations, nbhd size=1, neg = 0 0369: dt=25.600000, rms=0.471 (0.143%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 10 iterations, nbhd size=1, neg = 0 0370: dt=25.600000, rms=0.471 (0.160%), neg=0, invalid=762 iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 0371: dt=25.600000, rms=0.470 (0.089%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 5 iterations, nbhd size=0, neg = 0 0372: dt=25.600000, rms=0.470 (0.069%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0373: dt=32.000000, rms=0.469 (0.116%), neg=0, invalid=762 0374: dt=11.200000, rms=0.469 (-0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=762 0375: dt=44.800000, rms=0.466 (0.730%), neg=0, invalid=762 0376: dt=25.600000, rms=0.465 (0.356%), neg=0, invalid=762 0377: dt=25.600000, rms=0.464 (0.119%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0378: dt=25.600000, rms=0.463 (0.154%), neg=0, invalid=762 0379: dt=25.600000, rms=0.463 (0.152%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0380: dt=25.600000, rms=0.462 (0.141%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0381: dt=25.600000, rms=0.461 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0382: dt=25.600000, rms=0.461 (0.037%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0383: dt=25.600000, rms=0.461 (0.007%), neg=0, invalid=762 0384: dt=11.200000, rms=0.461 (0.043%), neg=0, invalid=762 0385: dt=102.400000, rms=0.460 (0.110%), neg=0, invalid=762 0386: dt=11.200000, rms=0.460 (0.009%), neg=0, invalid=762 0387: dt=11.200000, rms=0.460 (0.028%), neg=0, invalid=762 0388: dt=11.200000, rms=0.460 (0.015%), neg=0, invalid=762 0389: dt=11.200000, rms=0.460 (0.015%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0390: dt=0.000000, rms=0.466 (0.092%), neg=0, invalid=762 0391: dt=0.000000, rms=0.466 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=762 0392: dt=2.285714, rms=0.466 (0.109%), neg=0, invalid=762 0393: dt=0.864000, rms=0.466 (0.003%), neg=0, invalid=762 0394: dt=0.864000, rms=0.466 (0.001%), neg=0, invalid=762 0395: dt=0.864000, rms=0.466 (-0.010%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.478, neg=0, invalid=762 0396: dt=1.024000, rms=0.477 (0.240%), neg=0, invalid=762 0397: dt=0.256000, rms=0.477 (0.008%), neg=0, invalid=762 0398: dt=0.256000, rms=0.477 (-0.007%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=762 0399: dt=1.536000, rms=0.476 (0.295%), neg=0, invalid=762 0400: dt=0.448000, rms=0.476 (0.022%), neg=0, invalid=762 0401: dt=0.448000, rms=0.476 (0.009%), neg=0, invalid=762 0402: dt=0.448000, rms=0.476 (-0.010%), 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=0.467, neg=0, invalid=762 iter 0, gcam->neg = 523 after 12 iterations, nbhd size=1, neg = 0 0403: dt=2.308143, rms=0.435 (6.791%), neg=0, invalid=762 0404: dt=0.112000, rms=0.435 (0.100%), neg=0, invalid=762 0405: dt=0.112000, rms=0.435 (-0.104%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.435, neg=0, invalid=762 0406: dt=0.080000, rms=0.434 (0.161%), neg=0, invalid=762 0407: dt=0.000000, rms=0.434 (-0.001%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0408: dt=0.000000, rms=0.419 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0409: dt=27.744000, rms=0.419 (0.001%), neg=0, invalid=762 0410: dt=8.092000, rms=0.419 (0.000%), neg=0, invalid=762 0411: dt=8.092000, rms=0.419 (0.000%), neg=0, invalid=762 0412: dt=8.092000, rms=0.419 (-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=0.420, neg=0, invalid=762 0413: dt=0.000000, rms=0.420 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0414: dt=36.288000, rms=0.419 (0.029%), neg=0, invalid=762 0415: dt=82.944000, rms=0.419 (0.022%), neg=0, invalid=762 0416: dt=82.944000, rms=0.419 (0.030%), neg=0, invalid=762 0417: dt=82.944000, rms=0.419 (0.029%), neg=0, invalid=762 0418: dt=82.944000, rms=0.419 (0.016%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=762 0419: dt=11.200000, rms=0.419 (0.055%), neg=0, invalid=762 0420: dt=6.400000, rms=0.419 (0.011%), neg=0, invalid=762 0421: dt=6.400000, rms=0.419 (0.005%), neg=0, invalid=762 0422: dt=6.400000, rms=0.419 (-0.015%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.419, neg=0, invalid=762 0423: dt=63.676768, rms=0.417 (0.611%), neg=0, invalid=762 0424: dt=23.880597, rms=0.416 (0.272%), neg=0, invalid=762 0425: dt=44.800000, rms=0.415 (0.139%), neg=0, invalid=762 0426: dt=44.800000, rms=0.415 (0.130%), neg=0, invalid=762 0427: dt=44.800000, rms=0.414 (0.254%), neg=0, invalid=762 0428: dt=44.800000, rms=0.413 (0.190%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 10 iterations, nbhd size=1, neg = 0 0429: dt=44.800000, rms=0.412 (0.252%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0430: dt=44.800000, rms=0.411 (0.182%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0431: dt=44.800000, rms=0.410 (0.137%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 2 iterations, nbhd size=0, neg = 0 0432: dt=44.800000, rms=0.410 (0.183%), neg=0, invalid=762 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0433: dt=44.800000, rms=0.409 (0.095%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0434: dt=44.800000, rms=0.409 (0.103%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0435: dt=44.800000, rms=0.408 (0.101%), neg=0, invalid=762 0436: dt=25.600000, rms=0.408 (0.015%), neg=0, invalid=762 0437: dt=25.600000, rms=0.408 (0.017%), neg=0, invalid=762 0438: dt=25.600000, rms=0.408 (0.016%), neg=0, invalid=762 0439: dt=25.600000, rms=0.408 (0.011%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0440: dt=0.000703, rms=0.413 (0.000%), neg=0, invalid=762 0441: dt=0.000703, rms=0.413 (0.000%), neg=0, invalid=762 0442: dt=0.000703, rms=0.413 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=762 0443: dt=2.880000, rms=0.413 (0.017%), neg=0, invalid=762 0444: dt=1.008000, rms=0.413 (0.002%), neg=0, invalid=762 0445: dt=1.008000, rms=0.413 (0.000%), neg=0, invalid=762 0446: dt=1.008000, rms=0.413 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0447: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.422, neg=0, invalid=762 0448: dt=0.000000, rms=0.422 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.407, neg=0, invalid=762 iter 0, gcam->neg = 386 after 14 iterations, nbhd size=1, neg = 0 0449: dt=1.331361, rms=0.398 (2.218%), neg=0, invalid=762 0450: dt=0.000023, rms=0.398 (0.000%), neg=0, invalid=762 0451: dt=0.000023, rms=0.398 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.398, neg=0, invalid=762 0452: dt=0.112000, rms=0.398 (0.066%), neg=0, invalid=762 0453: dt=0.080000, rms=0.397 (0.017%), neg=0, invalid=762 0454: dt=0.080000, rms=0.397 (0.007%), neg=0, invalid=762 0455: dt=0.080000, rms=0.397 (-0.032%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 2 hours, 7 minutes and 43 seconds. mri_ca_register utimesec 7638.018170 mri_ca_register stimesec 24.121211 mri_ca_register ru_maxrss 1341096 mri_ca_register ru_ixrss 0 mri_ca_register ru_idrss 0 mri_ca_register ru_isrss 0 mri_ca_register ru_minflt 31356840 mri_ca_register ru_majflt 0 mri_ca_register ru_nswap 0 mri_ca_register ru_inblock 0 mri_ca_register ru_oublock 63392 mri_ca_register ru_msgsnd 0 mri_ca_register ru_msgrcv 0 mri_ca_register ru_nsignals 0 mri_ca_register ru_nvcsw 1907 mri_ca_register ru_nivcsw 3192 FSRUNTIME@ mri_ca_register 2.1287 hours 1 threads #-------------------------------------- #@# SubCort Seg Thu Sep 26 21:00:53 EDT 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == 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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 8.17 Atlas used for the 3D morph was /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 = 0.12654 (18) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (2512 voxels, overlap=0.811) Left_Lateral_Ventricle (4): linear fit = 0.87 x + 0.0 (2512 voxels, peak = 17), gca=17.3 gca peak = 0.17677 (13) mri peak = 0.12255 (17) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (3261 voxels, overlap=0.823) Right_Lateral_Ventricle (43): linear fit = 1.12 x + 0.0 (3261 voxels, peak = 14), gca=14.5 gca peak = 0.28129 (95) mri peak = 0.10842 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (680 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (680 voxels, peak = 95), gca=94.5 gca peak = 0.16930 (96) mri peak = 0.11323 (101) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (913 voxels, overlap=0.369) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (913 voxels, peak = 103), gca=103.2 gca peak = 0.24553 (55) mri peak = 0.10392 (70) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1133 voxels, overlap=0.065) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (1133 voxels, peak = 67), gca=67.4 gca peak = 0.30264 (59) mri peak = 0.09224 (75) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (973 voxels, overlap=0.019) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (973 voxels, peak = 76), gca=76.4 gca peak = 0.07580 (103) mri peak = 0.15057 (105) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (60839 voxels, overlap=0.597) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (60839 voxels, peak = 105), gca=104.5 gca peak = 0.07714 (104) mri peak = 0.13340 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (67114 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (67114 voxels, peak = 104), gca=104.0 gca peak = 0.09712 (58) mri peak = 0.03722 (72) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (34022 voxels, overlap=0.199) Left_Cerebral_Cortex (3): linear fit = 1.25 x + 0.0 (34022 voxels, peak = 72), gca=72.2 gca peak = 0.11620 (58) mri peak = 0.04059 (72) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (33510 voxels, overlap=0.008) Right_Cerebral_Cortex (42): linear fit = 1.29 x + 0.0 (33510 voxels, peak = 75), gca=75.1 gca peak = 0.30970 (66) mri peak = 0.11563 (81) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1401 voxels, overlap=0.021) Right_Caudate (50): linear fit = 1.21 x + 0.0 (1401 voxels, peak = 80), gca=79.5 gca peak = 0.15280 (69) mri peak = 0.11917 (80) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1351 voxels, overlap=0.428) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1351 voxels, peak = 78), gca=77.6 gca peak = 0.13902 (56) mri peak = 0.04500 (62) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (23642 voxels, overlap=0.864) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (23642 voxels, peak = 64), gca=63.6 gca peak = 0.14777 (55) mri peak = 0.04347 (68) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (29560 voxels, overlap=0.440) Right_Cerebellum_Cortex (47): linear fit = 1.25 x + 0.0 (29560 voxels, peak = 68), gca=68.5 gca peak = 0.16765 (84) mri peak = 0.09547 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8145 voxels, overlap=0.729) Left_Cerebellum_White_Matter (7): linear fit = 1.07 x + 0.0 (8145 voxels, peak = 89), gca=89.5 gca peak = 0.18739 (84) mri peak = 0.11277 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6309 voxels, overlap=0.742) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (6309 voxels, peak = 88), gca=87.8 gca peak = 0.29869 (57) mri peak = 0.09434 (78) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (582 voxels, overlap=0.061) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (582 voxels, peak = 77), gca=76.7 gca peak = 0.33601 (57) mri peak = 0.10183 (73) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (732 voxels, overlap=0.053) Right_Amygdala (54): linear fit = 1.25 x + 0.0 (732 voxels, peak = 72), gca=71.5 gca peak = 0.11131 (90) mri peak = 0.06586 (92) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5041 voxels, overlap=0.788) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5041 voxels, peak = 95), gca=94.9 gca peak = 0.11793 (83) mri peak = 0.08787 (84) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5849 voxels, overlap=0.920) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5849 voxels, peak = 85), gca=85.1 gca peak = 0.08324 (81) mri peak = 0.06983 (88) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2105 voxels, overlap=0.430) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2105 voxels, peak = 91), gca=91.1 gca peak = 0.10360 (77) mri peak = 0.09667 (88) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2261 voxels, overlap=0.444) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2261 voxels, peak = 84), gca=83.5 gca peak = 0.08424 (78) mri peak = 0.09269 (87) Brain_Stem (16): linear fit = 1.08 x + 0.0 (14448 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.08 x + 0.0 (14448 voxels, peak = 84), gca=83.9 gca peak = 0.12631 (89) mri peak = 0.08748 (89) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1901 voxels, overlap=0.791) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1901 voxels, peak = 91), gca=91.2 gca peak = 0.14500 (87) mri peak = 0.08452 (97) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1727 voxels, overlap=0.726) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1727 voxels, peak = 94), gca=93.5 gca peak = 0.14975 (24) mri peak = 0.20833 (21) gca peak = 0.19357 (14) mri peak = 0.12952 (18) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (410 voxels, overlap=0.677) Fourth_Ventricle (15): linear fit = 1.18 x + 0.0 (410 voxels, peak = 17), gca=16.6 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 1.28 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 1.05 x + 0.0 Left_Pallidum too bright - rescaling by 0.980 (from 1.075) to 101.1 (was 103.2) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.17217 (16) mri peak = 0.12654 (18) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2512 voxels, overlap=0.921) Left_Lateral_Ventricle (4): linear fit = 1.01 x + 0.0 (2512 voxels, peak = 16), gca=16.2 gca peak = 0.17255 (14) mri peak = 0.12255 (17) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3261 voxels, overlap=0.743) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (3261 voxels, peak = 14), gca=14.5 gca peak = 0.28191 (93) mri peak = 0.10842 (96) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (680 voxels, overlap=1.011) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (680 voxels, peak = 93), gca=92.5 gca peak = 0.17533 (101) mri peak = 0.11323 (101) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (913 voxels, overlap=0.977) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (913 voxels, peak = 104), gca=103.5 gca peak = 0.25307 (68) mri peak = 0.10392 (70) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1133 voxels, overlap=1.003) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1133 voxels, peak = 69), gca=69.0 gca peak = 0.25438 (73) mri peak = 0.09224 (75) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (973 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 0.99 x + 0.0 (973 voxels, peak = 72), gca=71.9 gca peak = 0.07772 (104) mri peak = 0.15057 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (60839 voxels, overlap=0.662) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (60839 voxels, peak = 104), gca=104.0 gca peak = 0.07714 (104) mri peak = 0.13340 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (67114 voxels, overlap=0.612) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (67114 voxels, peak = 104), gca=104.0 gca peak = 0.07951 (72) mri peak = 0.03722 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34022 voxels, overlap=0.973) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (34022 voxels, peak = 70), gca=70.2 gca peak = 0.09110 (75) mri peak = 0.04059 (72) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33510 voxels, overlap=0.960) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (33510 voxels, peak = 74), gca=73.9 gca peak = 0.21545 (80) mri peak = 0.11563 (81) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1401 voxels, overlap=1.001) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1401 voxels, peak = 80), gca=80.0 gca peak = 0.16641 (87) mri peak = 0.11917 (80) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1351 voxels, overlap=0.833) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1351 voxels, peak = 85), gca=84.8 gca peak = 0.12405 (63) mri peak = 0.04500 (62) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (23642 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (23642 voxels, peak = 62), gca=62.1 gca peak = 0.12395 (68) mri peak = 0.04347 (68) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (29560 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (29560 voxels, peak = 66), gca=66.3 gca peak = 0.15873 (90) mri peak = 0.09547 (88) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8145 voxels, overlap=0.959) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (8145 voxels, peak = 90), gca=89.6 gca peak = 0.16906 (88) mri peak = 0.11277 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6309 voxels, overlap=0.921) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6309 voxels, peak = 88), gca=87.6 gca peak = 0.27968 (78) mri peak = 0.09434 (78) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (582 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.98 x + 0.0 (582 voxels, peak = 76), gca=76.1 gca peak = 0.28268 (71) mri peak = 0.10183 (73) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (732 voxels, overlap=1.008) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (732 voxels, peak = 73), gca=73.5 gca peak = 0.10686 (95) mri peak = 0.06586 (92) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5041 voxels, overlap=0.953) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5041 voxels, peak = 95), gca=94.5 gca peak = 0.11628 (85) mri peak = 0.08787 (84) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5849 voxels, overlap=0.974) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5849 voxels, peak = 85), gca=84.6 gca peak = 0.09344 (91) mri peak = 0.06983 (88) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2105 voxels, overlap=0.905) Left_Putamen (12): linear fit = 1.01 x + 0.0 (2105 voxels, peak = 92), gca=92.4 gca peak = 0.08953 (85) mri peak = 0.09667 (88) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2261 voxels, overlap=0.835) Right_Putamen (51): linear fit = 1.01 x + 0.0 (2261 voxels, peak = 86), gca=86.3 gca peak = 0.08924 (84) mri peak = 0.09269 (87) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14448 voxels, overlap=0.742) Brain_Stem (16): linear fit = 1.00 x + 0.0 (14448 voxels, peak = 84), gca=83.6 gca peak = 0.11452 (91) mri peak = 0.08748 (89) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1901 voxels, overlap=0.821) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1901 voxels, peak = 91), gca=90.5 gca peak = 0.16257 (92) mri peak = 0.08452 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1727 voxels, overlap=0.916) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1727 voxels, peak = 92), gca=92.5 gca peak = 0.16538 (27) mri peak = 0.20833 (21) gca peak = 0.17387 (17) mri peak = 0.12952 (18) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (410 voxels, overlap=0.809) Fourth_Ventricle (15): linear fit = 1.09 x + 0.0 (410 voxels, peak = 18), gca=18.4 gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.17751 (35) gca peak Left_Thalamus = 0.36646 (102) gca peak Third_Ventricle = 0.16538 (27) gca peak CSF = 0.23378 (38) gca peak Left_Accumbens_area = 0.66223 (70) 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 = 0.20093 (28) gca peak Right_Accumbens_area = 0.31280 (78) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.54107 (34) gca peak WM_hypointensities = 0.07930 (76) gca peak non_WM_hypointensities = 0.09318 (44) gca peak Optic_Chiasm = 0.70852 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.974 (from 1.025) to 100.9 (was 103.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 95545 voxels changed in iteration 0 of unlikely voxel relabeling 436 voxels changed in iteration 1 of unlikely voxel relabeling 49 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 96761 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 651 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 91619 changed. image ll: -2.158, PF=0.500 pass 2: 23514 changed. image ll: -2.156, PF=0.500 pass 3: 6770 changed. pass 4: 2336 changed. 79585 voxels changed in iteration 0 of unlikely voxel relabeling 774 voxels changed in iteration 1 of unlikely voxel relabeling 23 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 9469 voxels changed in iteration 0 of unlikely voxel relabeling 149 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 8440 voxels changed in iteration 0 of unlikely voxel relabeling 110 voxels changed in iteration 1 of unlikely voxel relabeling 12 voxels changed in iteration 2 of unlikely voxel relabeling 8 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling 7212 voxels changed in iteration 0 of unlikely voxel relabeling 41 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3482.184767 mri_ca_label stimesec 7.890093 mri_ca_label ru_maxrss 2104888 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 8983374 mri_ca_label ru_majflt 0 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 0 mri_ca_label ru_oublock 552 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 146 mri_ca_label ru_nivcsw 1249 auto-labeling took 58 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/cc_up.lta BIO-ALS-701-088-BL will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/norm.mgz 71490 voxels in left wm, 120530 in right wm, xrange [119, 136] searching rotation angles z=[-14 -0], y=[-5 9] searching scale 1 Z rot -14.2 searching scale 1 Z rot -13.9 searching scale 1 Z rot -13.7 searching scale 1 Z rot -13.4 searching scale 1 Z rot -13.2 searching scale 1 Z rot -12.9 searching scale 1 Z rot -12.7 searching scale 1 Z rot -12.4 searching scale 1 Z rot -12.2 searching scale 1 Z rot -11.9 searching scale 1 Z rot -11.7 searching scale 1 Z rot -11.4 searching scale 1 Z rot -11.2 searching scale 1 Z rot -10.9 searching scale 1 Z rot -10.7 searching scale 1 Z rot -10.4 searching scale 1 Z rot -10.2 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.7 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.2 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.7 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 global minimum found at slice 129.0, rotations (2.32, -6.94) final transformation (x=129.0, yr=2.317, zr=-6.937): 0.99187 0.12078 0.04013 -18.41839; -0.12069 0.99268 -0.00488 23.92311; -0.04043 0.00000 0.99918 37.29358; 0.00000 0.00000 0.00000 1.00000; updating x range to be [125, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 121 96 eigenvectors: -0.00208 -0.00049 1.00000; -0.22753 -0.97377 -0.00095; 0.97377 -0.22753 0.00192; writing aseg with callosum to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aseg.auto.mgz... corpus callosum segmentation took 1.5 minutes #-------------------------------------- #@# Merge ASeg Thu Sep 26 22:00:34 EDT 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Sep 26 22:00:34 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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... 1157 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 109 gm peak at 82 (82), valley at 33 (33) csf peak at 18, setting threshold to 60 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 78 (78), valley at 32 (32) csf peak at 19, setting threshold to 58 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 46 seconds. #-------------------------------------------- #@# Mask BFS Thu Sep 26 22:03:23 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1916902 voxels in mask (pct= 11.43) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Sep 26 22:03:25 EDT 2019 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.0 +- 6.4 [79.0 --> 125.0] GM (73.0) : 70.9 +- 11.3 [30.0 --> 95.0] setting bottom of white matter range to 82.2 setting top of gray matter range to 93.6 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 8993 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5487 filled 3778 bright non-wm voxels segmented. 4497 diagonally connected voxels added... white matter segmentation took 1.5 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 0.41 minutes reading wm segmentation from wm.seg.mgz... 274 voxels added to wm to prevent paths from MTL structures to cortex 3418 additional wm voxels added 0 additional wm voxels added SEG EDIT: 57380 voxels turned on, 51760 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 34 found - 34 modified | TOTAL: 34 pass 2 (xy+): 0 found - 34 modified | TOTAL: 34 pass 1 (xy-): 34 found - 34 modified | TOTAL: 68 pass 2 (xy-): 0 found - 34 modified | TOTAL: 68 pass 1 (yz+): 45 found - 45 modified | TOTAL: 113 pass 2 (yz+): 0 found - 45 modified | TOTAL: 113 pass 1 (yz-): 33 found - 33 modified | TOTAL: 146 pass 2 (yz-): 0 found - 33 modified | TOTAL: 146 pass 1 (xz+): 24 found - 24 modified | TOTAL: 170 pass 2 (xz+): 0 found - 24 modified | TOTAL: 170 pass 1 (xz-): 29 found - 29 modified | TOTAL: 199 pass 2 (xz-): 0 found - 29 modified | TOTAL: 199 Iteration Number : 1 pass 1 (+++): 41 found - 41 modified | TOTAL: 41 pass 2 (+++): 0 found - 41 modified | TOTAL: 41 pass 1 (+++): 26 found - 26 modified | TOTAL: 67 pass 2 (+++): 0 found - 26 modified | TOTAL: 67 pass 1 (+++): 56 found - 56 modified | TOTAL: 123 pass 2 (+++): 0 found - 56 modified | TOTAL: 123 pass 1 (+++): 58 found - 58 modified | TOTAL: 181 pass 2 (+++): 0 found - 58 modified | TOTAL: 181 Iteration Number : 1 pass 1 (++): 101 found - 101 modified | TOTAL: 101 pass 2 (++): 0 found - 101 modified | TOTAL: 101 pass 1 (+-): 87 found - 87 modified | TOTAL: 188 pass 2 (+-): 0 found - 87 modified | TOTAL: 188 pass 1 (--): 96 found - 96 modified | TOTAL: 284 pass 2 (--): 0 found - 96 modified | TOTAL: 284 pass 1 (-+): 89 found - 89 modified | TOTAL: 373 pass 2 (-+): 0 found - 89 modified | TOTAL: 373 Iteration Number : 2 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 12 found - 12 modified | TOTAL: 24 pass 2 (xy-): 0 found - 12 modified | TOTAL: 24 pass 1 (yz+): 11 found - 11 modified | TOTAL: 35 pass 2 (yz+): 0 found - 11 modified | TOTAL: 35 pass 1 (yz-): 4 found - 4 modified | TOTAL: 39 pass 2 (yz-): 0 found - 4 modified | TOTAL: 39 pass 1 (xz+): 11 found - 11 modified | TOTAL: 50 pass 2 (xz+): 0 found - 11 modified | TOTAL: 50 pass 1 (xz-): 6 found - 6 modified | TOTAL: 56 pass 2 (xz-): 0 found - 6 modified | TOTAL: 56 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 6 found - 6 modified | TOTAL: 8 pass 2 (+++): 0 found - 6 modified | TOTAL: 8 pass 1 (+++): 2 found - 2 modified | TOTAL: 10 pass 2 (+++): 0 found - 2 modified | TOTAL: 10 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 3 found - 3 modified | TOTAL: 5 pass 2 (+-): 0 found - 3 modified | TOTAL: 5 pass 1 (--): 3 found - 3 modified | TOTAL: 8 pass 2 (--): 0 found - 3 modified | TOTAL: 8 pass 1 (-+): 1 found - 1 modified | TOTAL: 9 pass 2 (-+): 0 found - 1 modified | TOTAL: 9 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 = 832 (out of 769955: 0.108058) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Sep 26 22:05:23 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.99528 0.08338 0.05024 -17.34076; -0.10262 0.94157 0.41929 -35.83389; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 0.99528 0.08338 0.05024 -17.34076; -0.10262 0.94157 0.41929 -35.83389; -0.01115 -0.39944 0.85657 67.01196; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1258 (min = 350, max = 1400), aspect = 0.45 (min = 0.10, max = 0.75) no need to search using seed (127, 121, 152), TAL = (1.0, 24.0, 7.0) talairach voxel to voxel transform 0.99497 -0.09346 -0.01261 14.74946; 0.08502 0.87145 -0.43156 61.62120; 0.05260 0.40517 0.96604 -49.30544; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (127, 121, 152) --> (1.0, 24.0, 7.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (1.00, 24.00, 7.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 24.00, 7.00) SRC: (109.98, 110.74, 152.29) search lh wm seed point around talairach space (-17.00, 24.00, 7.00), SRC: (145.80, 113.80, 154.18) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Thu Sep 26 22:05:54 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 3 found - 3 modified | TOTAL: 7 pass 2 (yz-): 0 found - 3 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 0 found - 0 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 372253: 0.003492) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 213 vertices, 261 faces slice 40: 5379 vertices, 5683 faces slice 50: 16069 vertices, 16536 faces slice 60: 30907 vertices, 31459 faces slice 70: 47353 vertices, 47914 faces slice 80: 62724 vertices, 63209 faces slice 90: 76600 vertices, 77128 faces slice 100: 90112 vertices, 90645 faces slice 110: 103577 vertices, 104077 faces slice 120: 115592 vertices, 116112 faces slice 130: 127888 vertices, 128412 faces slice 140: 139966 vertices, 140519 faces slice 150: 150741 vertices, 151208 faces slice 160: 160391 vertices, 160896 faces slice 170: 169308 vertices, 169726 faces slice 180: 175805 vertices, 176189 faces slice 190: 181311 vertices, 181617 faces slice 200: 184374 vertices, 184561 faces slice 210: 184432 vertices, 184600 faces slice 220: 184432 vertices, 184600 faces slice 230: 184432 vertices, 184600 faces slice 240: 184432 vertices, 184600 faces slice 250: 184432 vertices, 184600 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 184432 voxel in cpt #1: X=-168 [v=184432,e=553800,f=369200] located at (-28.451521, -23.661777, -1.743412) For the whole surface: X=-168 [v=184432,e=553800,f=369200] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Thu Sep 26 22:06:01 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 3 found - 3 modified | TOTAL: 4 pass 2 (xy-): 0 found - 3 modified | TOTAL: 4 pass 1 (yz+): 1 found - 1 modified | TOTAL: 5 pass 2 (yz+): 0 found - 1 modified | TOTAL: 5 pass 1 (yz-): 0 found - 0 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 10 (out of 375912: 0.002660) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ slice 30: 271 vertices, 330 faces slice 40: 6523 vertices, 6866 faces slice 50: 18913 vertices, 19400 faces slice 60: 34413 vertices, 34956 faces slice 70: 51037 vertices, 51625 faces slice 80: 66896 vertices, 67395 faces slice 90: 80733 vertices, 81259 faces slice 100: 94988 vertices, 95519 faces slice 110: 108627 vertices, 109164 faces slice 120: 120893 vertices, 121441 faces slice 130: 132749 vertices, 133293 faces slice 140: 144193 vertices, 144705 faces slice 150: 154504 vertices, 155006 faces slice 160: 164176 vertices, 164654 faces slice 170: 171275 vertices, 171657 faces slice 180: 177962 vertices, 178290 faces slice 190: 182509 vertices, 182804 faces slice 200: 185010 vertices, 185189 faces slice 210: 185054 vertices, 185214 faces slice 220: 185054 vertices, 185214 faces slice 230: 185054 vertices, 185214 faces slice 240: 185054 vertices, 185214 faces slice 250: 185054 vertices, 185214 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 185054 voxel in cpt #1: X=-160 [v=185054,e=555642,f=370428] located at (27.745983, -26.409384, 4.517400) For the whole surface: X=-160 [v=185054,e=555642,f=370428] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Sep 26 22:06:08 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Thu Sep 26 22:06:13 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Thu Sep 26 22:06:20 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 52.0 mm, total surface area = 96433 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.161 (target=0.015) step 005: RMS=0.123 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.072 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.060 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.053 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.047 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 37.339997 mris_inflate stimesec 0.183990 mris_inflate ru_maxrss 235824 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 149656 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 12984 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 581 mris_inflate ru_nivcsw 19 #-------------------------------------------- #@# Inflation1 rh Thu Sep 26 22:06:57 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 52.0 mm, total surface area = 96435 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.6 minutes step 000: RMS=0.162 (target=0.015) step 005: RMS=0.124 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.082 (target=0.015) step 020: RMS=0.073 (target=0.015) step 025: RMS=0.065 (target=0.015) step 030: RMS=0.061 (target=0.015) step 035: RMS=0.056 (target=0.015) step 040: RMS=0.054 (target=0.015) step 045: RMS=0.052 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.050 (target=0.015) inflation complete. Not saving sulc mris_inflate utimesec 37.395181 mris_inflate stimesec 0.278031 mris_inflate ru_maxrss 236252 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 210730 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13024 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 553 mris_inflate ru_nivcsw 307 #-------------------------------------------- #@# QSphere lh Thu Sep 26 22:07:35 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.56 (0.00-->6.88) (max @ vno 144172 --> 144200) face area 0.02 +- 0.03 (-0.15-->0.62) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.284... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.848, avgs=0 005/300: dt: 0.9000, rms radial error=175.594, avgs=0 010/300: dt: 0.9000, rms radial error=175.043, avgs=0 015/300: dt: 0.9000, rms radial error=174.312, avgs=0 020/300: dt: 0.9000, rms radial error=173.481, avgs=0 025/300: dt: 0.9000, rms radial error=172.592, avgs=0 030/300: dt: 0.9000, rms radial error=171.671, avgs=0 035/300: dt: 0.9000, rms radial error=170.734, avgs=0 040/300: dt: 0.9000, rms radial error=169.788, avgs=0 045/300: dt: 0.9000, rms radial error=168.841, avgs=0 050/300: dt: 0.9000, rms radial error=167.893, avgs=0 055/300: dt: 0.9000, rms radial error=166.949, avgs=0 060/300: dt: 0.9000, rms radial error=166.007, avgs=0 065/300: dt: 0.9000, rms radial error=165.071, avgs=0 070/300: dt: 0.9000, rms radial error=164.138, avgs=0 075/300: dt: 0.9000, rms radial error=163.211, avgs=0 080/300: dt: 0.9000, rms radial error=162.289, avgs=0 085/300: dt: 0.9000, rms radial error=161.372, avgs=0 090/300: dt: 0.9000, rms radial error=160.461, avgs=0 095/300: dt: 0.9000, rms radial error=159.554, avgs=0 100/300: dt: 0.9000, rms radial error=158.652, avgs=0 105/300: dt: 0.9000, rms radial error=157.756, avgs=0 110/300: dt: 0.9000, rms radial error=156.864, avgs=0 115/300: dt: 0.9000, rms radial error=155.977, avgs=0 120/300: dt: 0.9000, rms radial error=155.096, avgs=0 125/300: dt: 0.9000, rms radial error=154.219, avgs=0 130/300: dt: 0.9000, rms radial error=153.349, avgs=0 135/300: dt: 0.9000, rms radial error=152.484, avgs=0 140/300: dt: 0.9000, rms radial error=151.624, avgs=0 145/300: dt: 0.9000, rms radial error=150.768, avgs=0 150/300: dt: 0.9000, rms radial error=149.917, avgs=0 155/300: dt: 0.9000, rms radial error=149.074, avgs=0 160/300: dt: 0.9000, rms radial error=148.236, avgs=0 165/300: dt: 0.9000, rms radial error=147.403, avgs=0 170/300: dt: 0.9000, rms radial error=146.574, avgs=0 175/300: dt: 0.9000, rms radial error=145.750, avgs=0 180/300: dt: 0.9000, rms radial error=144.931, avgs=0 185/300: dt: 0.9000, rms radial error=144.115, avgs=0 190/300: dt: 0.9000, rms radial error=143.305, avgs=0 195/300: dt: 0.9000, rms radial error=142.499, avgs=0 200/300: dt: 0.9000, rms radial error=141.697, avgs=0 205/300: dt: 0.9000, rms radial error=140.900, avgs=0 210/300: dt: 0.9000, rms radial error=140.107, avgs=0 215/300: dt: 0.9000, rms radial error=139.319, avgs=0 220/300: dt: 0.9000, rms radial error=138.535, avgs=0 225/300: dt: 0.9000, rms radial error=137.755, avgs=0 230/300: dt: 0.9000, rms radial error=136.980, avgs=0 235/300: dt: 0.9000, rms radial error=136.209, avgs=0 240/300: dt: 0.9000, rms radial error=135.442, avgs=0 245/300: dt: 0.9000, rms radial error=134.679, avgs=0 250/300: dt: 0.9000, rms radial error=133.922, avgs=0 255/300: dt: 0.9000, rms radial error=133.169, avgs=0 260/300: dt: 0.9000, rms radial error=132.421, avgs=0 265/300: dt: 0.9000, rms radial error=131.676, avgs=0 270/300: dt: 0.9000, rms radial error=130.936, avgs=0 275/300: dt: 0.9000, rms radial error=130.200, avgs=0 280/300: dt: 0.9000, rms radial error=129.468, avgs=0 285/300: dt: 0.9000, rms radial error=128.740, avgs=0 290/300: dt: 0.9000, rms radial error=128.016, avgs=0 295/300: dt: 0.9000, rms radial error=127.297, avgs=0 300/300: dt: 0.9000, rms radial error=126.581, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 22270.87 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 2 (K=40.0), pass 1, starting sse = 4028.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00000 epoch 3 (K=160.0), pass 1, starting sse = 496.34 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00250 epoch 4 (K=640.0), pass 1, starting sse = 50.56 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00660 final distance error %30.36 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 219.010338 mris_sphere stimesec 0.232973 mris_sphere ru_maxrss 236020 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 255961 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12984 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 403 mris_sphere ru_nivcsw 61 FSRUNTIME@ mris_sphere 0.0609 hours 1 threads #-------------------------------------------- #@# QSphere rh Thu Sep 26 22:11:14 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.86 +- 0.56 (0.00-->10.75) (max @ vno 105313 --> 105328) face area 0.02 +- 0.03 (-0.33-->0.66) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.287... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.721, avgs=0 005/300: dt: 0.9000, rms radial error=175.464, avgs=0 010/300: dt: 0.9000, rms radial error=174.914, avgs=0 015/300: dt: 0.9000, rms radial error=174.190, avgs=0 020/300: dt: 0.9000, rms radial error=173.366, avgs=0 025/300: dt: 0.9000, rms radial error=172.484, avgs=0 030/300: dt: 0.9000, rms radial error=171.571, avgs=0 035/300: dt: 0.9000, rms radial error=170.640, avgs=0 040/300: dt: 0.9000, rms radial error=169.703, avgs=0 045/300: dt: 0.9000, rms radial error=168.763, avgs=0 050/300: dt: 0.9000, rms radial error=167.824, avgs=0 055/300: dt: 0.9000, rms radial error=166.886, avgs=0 060/300: dt: 0.9000, rms radial error=165.952, avgs=0 065/300: dt: 0.9000, rms radial error=165.022, avgs=0 070/300: dt: 0.9000, rms radial error=164.095, avgs=0 075/300: dt: 0.9000, rms radial error=163.174, avgs=0 080/300: dt: 0.9000, rms radial error=162.261, avgs=0 085/300: dt: 0.9000, rms radial error=161.351, avgs=0 090/300: dt: 0.9000, rms radial error=160.447, avgs=0 095/300: dt: 0.9000, rms radial error=159.546, avgs=0 100/300: dt: 0.9000, rms radial error=158.650, avgs=0 105/300: dt: 0.9000, rms radial error=157.759, avgs=0 110/300: dt: 0.9000, rms radial error=156.872, avgs=0 115/300: dt: 0.9000, rms radial error=155.989, avgs=0 120/300: dt: 0.9000, rms radial error=155.111, avgs=0 125/300: dt: 0.9000, rms radial error=154.240, avgs=0 130/300: dt: 0.9000, rms radial error=153.374, avgs=0 135/300: dt: 0.9000, rms radial error=152.513, avgs=0 140/300: dt: 0.9000, rms radial error=151.657, avgs=0 145/300: dt: 0.9000, rms radial error=150.806, avgs=0 150/300: dt: 0.9000, rms radial error=149.959, avgs=0 155/300: dt: 0.9000, rms radial error=149.117, avgs=0 160/300: dt: 0.9000, rms radial error=148.280, avgs=0 165/300: dt: 0.9000, rms radial error=147.447, avgs=0 170/300: dt: 0.9000, rms radial error=146.618, avgs=0 175/300: dt: 0.9000, rms radial error=145.794, avgs=0 180/300: dt: 0.9000, rms radial error=144.975, avgs=0 185/300: dt: 0.9000, rms radial error=144.161, avgs=0 190/300: dt: 0.9000, rms radial error=143.350, avgs=0 195/300: dt: 0.9000, rms radial error=142.544, avgs=0 200/300: dt: 0.9000, rms radial error=141.743, avgs=0 205/300: dt: 0.9000, rms radial error=140.946, avgs=0 210/300: dt: 0.9000, rms radial error=140.154, avgs=0 215/300: dt: 0.9000, rms radial error=139.366, avgs=0 220/300: dt: 0.9000, rms radial error=138.582, avgs=0 225/300: dt: 0.9000, rms radial error=137.803, avgs=0 230/300: dt: 0.9000, rms radial error=137.028, avgs=0 235/300: dt: 0.9000, rms radial error=136.257, avgs=0 240/300: dt: 0.9000, rms radial error=135.491, avgs=0 245/300: dt: 0.9000, rms radial error=134.729, avgs=0 250/300: dt: 0.9000, rms radial error=133.971, avgs=0 255/300: dt: 0.9000, rms radial error=133.218, avgs=0 260/300: dt: 0.9000, rms radial error=132.468, avgs=0 265/300: dt: 0.9000, rms radial error=131.723, avgs=0 270/300: dt: 0.9000, rms radial error=130.982, avgs=0 275/300: dt: 0.9000, rms radial error=130.246, avgs=0 280/300: dt: 0.9000, rms radial error=129.514, avgs=0 285/300: dt: 0.9000, rms radial error=128.785, avgs=0 290/300: dt: 0.9000, rms radial error=128.061, avgs=0 295/300: dt: 0.9000, rms radial error=127.341, avgs=0 300/300: dt: 0.9000, rms radial error=126.625, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 22275.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 2 (K=40.0), pass 1, starting sse = 3997.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00002 epoch 3 (K=160.0), pass 1, starting sse = 475.64 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00098 epoch 4 (K=640.0), pass 1, starting sse = 49.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00416 final distance error %30.27 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.06 hours mris_sphere utimesec 216.304924 mris_sphere stimesec 0.241973 mris_sphere ru_maxrss 236464 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 261550 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 13024 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 371 mris_sphere ru_nivcsw 62 FSRUNTIME@ mris_sphere 0.0602 hours 1 threads #-------------------------------------------- #@# Fix Topology Copy lh Thu Sep 26 22:14:51 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated #-------------------------------------------- #@# Fix Topology Copy rh Thu Sep 26 22:14:51 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated #@# Fix Topology lh Thu Sep 26 22:14:52 EDT 2019 mris_fix_topology -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BIO-ALS-701-088-BL lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-168 (nv=184432, nf=369200, ne=553800, g=85) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 17018 ambiguous faces found in tessellation segmenting defects... 71 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 4 -merging segment 15 into 4 69 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.1063 (-4.5531) -vertex loglikelihood: -5.9388 (-2.9694) -normal dot loglikelihood: -3.5818 (-3.5818) -quad curv loglikelihood: -6.3144 (-3.1572) Total Loglikelihood : -24.9412 CORRECTING DEFECT 0 (vertices=284, convex hull=248, v0=673) After retessellation of defect 0 (v0=673), euler #=-62 (174685,521326,346579) : difference with theory (-66) = -4 CORRECTING DEFECT 1 (vertices=21, convex hull=51, v0=2510) After retessellation of defect 1 (v0=2510), euler #=-61 (174692,521366,346613) : difference with theory (-65) = -4 CORRECTING DEFECT 2 (vertices=8, convex hull=18, v0=3385) After retessellation of defect 2 (v0=3385), euler #=-60 (174693,521376,346623) : difference with theory (-64) = -4 CORRECTING DEFECT 3 (vertices=47, convex hull=100, v0=5302) After retessellation of defect 3 (v0=5302), euler #=-59 (174721,521503,346723) : difference with theory (-63) = -4 CORRECTING DEFECT 4 (vertices=2377, convex hull=610, v0=7677) XL defect detected... After retessellation of defect 4 (v0=7677), euler #=-57 (174942,522476,347477) : difference with theory (-62) = -5 CORRECTING DEFECT 5 (vertices=8, convex hull=26, v0=9079) After retessellation of defect 5 (v0=9079), euler #=-56 (174942,522482,347484) : difference with theory (-61) = -5 CORRECTING DEFECT 6 (vertices=42, convex hull=99, v0=9306) After retessellation of defect 6 (v0=9306), euler #=-55 (174958,522573,347560) : difference with theory (-60) = -5 CORRECTING DEFECT 7 (vertices=30, convex hull=84, v0=9470) After retessellation of defect 7 (v0=9470), euler #=-54 (174972,522645,347619) : difference with theory (-59) = -5 CORRECTING DEFECT 8 (vertices=36, convex hull=65, v0=11229) After retessellation of defect 8 (v0=11229), euler #=-53 (174991,522728,347684) : difference with theory (-58) = -5 CORRECTING DEFECT 9 (vertices=47, convex hull=45, v0=19710) After retessellation of defect 9 (v0=19710), euler #=-52 (174994,522755,347709) : difference with theory (-57) = -5 CORRECTING DEFECT 10 (vertices=26, convex hull=44, v0=20050) After retessellation of defect 10 (v0=20050), euler #=-51 (175004,522801,347746) : difference with theory (-56) = -5 CORRECTING DEFECT 11 (vertices=5, convex hull=25, v0=22385) After retessellation of defect 11 (v0=22385), euler #=-50 (175004,522806,347752) : difference with theory (-55) = -5 CORRECTING DEFECT 12 (vertices=129, convex hull=101, v0=25624) After retessellation of defect 12 (v0=25624), euler #=-49 (175021,522906,347836) : difference with theory (-54) = -5 CORRECTING DEFECT 13 (vertices=17, convex hull=43, v0=28643) After retessellation of defect 13 (v0=28643), euler #=-48 (175024,522927,347855) : difference with theory (-53) = -5 CORRECTING DEFECT 14 (vertices=174, convex hull=80, v0=35198) After retessellation of defect 14 (v0=35198), euler #=-47 (175062,523076,347967) : difference with theory (-52) = -5 CORRECTING DEFECT 15 (vertices=30, convex hull=47, v0=35526) After retessellation of defect 15 (v0=35526), euler #=-46 (175080,523147,348021) : difference with theory (-51) = -5 CORRECTING DEFECT 16 (vertices=37, convex hull=56, v0=47368) After retessellation of defect 16 (v0=47368), euler #=-45 (175089,523199,348065) : difference with theory (-50) = -5 CORRECTING DEFECT 17 (vertices=77, convex hull=101, v0=51869) After retessellation of defect 17 (v0=51869), euler #=-44 (175136,523391,348211) : difference with theory (-49) = -5 CORRECTING DEFECT 18 (vertices=14, convex hull=28, v0=55432) After retessellation of defect 18 (v0=55432), euler #=-43 (175139,523411,348229) : difference with theory (-48) = -5 CORRECTING DEFECT 19 (vertices=28, convex hull=58, v0=60389) After retessellation of defect 19 (v0=60389), euler #=-42 (175152,523476,348282) : difference with theory (-47) = -5 CORRECTING DEFECT 20 (vertices=48, convex hull=86, v0=63866) After retessellation of defect 20 (v0=63866), euler #=-41 (175176,523589,348372) : difference with theory (-46) = -5 CORRECTING DEFECT 21 (vertices=24, convex hull=42, v0=64481) After retessellation of defect 21 (v0=64481), euler #=-40 (175185,523633,348408) : difference with theory (-45) = -5 CORRECTING DEFECT 22 (vertices=37, convex hull=70, v0=64912) After retessellation of defect 22 (v0=64912), euler #=-39 (175205,523721,348477) : difference with theory (-44) = -5 CORRECTING DEFECT 23 (vertices=7, convex hull=33, v0=73316) After retessellation of defect 23 (v0=73316), euler #=-38 (175207,523735,348490) : difference with theory (-43) = -5 CORRECTING DEFECT 24 (vertices=16, convex hull=25, v0=73922) After retessellation of defect 24 (v0=73922), euler #=-37 (175208,523749,348504) : difference with theory (-42) = -5 CORRECTING DEFECT 25 (vertices=13, convex hull=36, v0=77447) After retessellation of defect 25 (v0=77447), euler #=-36 (175210,523768,348522) : difference with theory (-41) = -5 CORRECTING DEFECT 26 (vertices=49, convex hull=32, v0=77685) After retessellation of defect 26 (v0=77685), euler #=-35 (175212,523783,348536) : difference with theory (-40) = -5 CORRECTING DEFECT 27 (vertices=457, convex hull=244, v0=78872) After retessellation of defect 27 (v0=78872), euler #=-34 (175223,523935,348678) : difference with theory (-39) = -5 CORRECTING DEFECT 28 (vertices=118, convex hull=100, v0=81329) After retessellation of defect 28 (v0=81329), euler #=-33 (175255,524074,348786) : difference with theory (-38) = -5 CORRECTING DEFECT 29 (vertices=36, convex hull=29, v0=82839) After retessellation of defect 29 (v0=82839), euler #=-32 (175264,524111,348815) : difference with theory (-37) = -5 CORRECTING DEFECT 30 (vertices=38, convex hull=52, v0=83694) After retessellation of defect 30 (v0=83694), euler #=-31 (175279,524177,348867) : difference with theory (-36) = -5 CORRECTING DEFECT 31 (vertices=36, convex hull=77, v0=91925) After retessellation of defect 31 (v0=91925), euler #=-30 (175300,524274,348944) : difference with theory (-35) = -5 CORRECTING DEFECT 32 (vertices=42, convex hull=40, v0=92159) After retessellation of defect 32 (v0=92159), euler #=-29 (175309,524317,348979) : difference with theory (-34) = -5 CORRECTING DEFECT 33 (vertices=9, convex hull=20, v0=93805) After retessellation of defect 33 (v0=93805), euler #=-28 (175309,524321,348984) : difference with theory (-33) = -5 CORRECTING DEFECT 34 (vertices=46, convex hull=89, v0=95505) After retessellation of defect 34 (v0=95505), euler #=-27 (175335,524434,349072) : difference with theory (-32) = -5 CORRECTING DEFECT 35 (vertices=31, convex hull=48, v0=98426) After retessellation of defect 35 (v0=98426), euler #=-26 (175350,524499,349123) : difference with theory (-31) = -5 CORRECTING DEFECT 36 (vertices=39, convex hull=56, v0=98504) After retessellation of defect 36 (v0=98504), euler #=-25 (175359,524551,349167) : difference with theory (-30) = -5 CORRECTING DEFECT 37 (vertices=3040, convex hull=776, v0=100634) XL defect detected... After retessellation of defect 37 (v0=100634), euler #=-27 (176272,527757,351458) : difference with theory (-29) = -2 CORRECTING DEFECT 38 (vertices=520, convex hull=574, v0=101765) L defect detected... After retessellation of defect 38 (v0=101765), euler #=-26 (176511,528749,352212) : difference with theory (-28) = -2 CORRECTING DEFECT 39 (vertices=32, convex hull=34, v0=110436) After retessellation of defect 39 (v0=110436), euler #=-25 (176516,528777,352236) : difference with theory (-27) = -2 CORRECTING DEFECT 40 (vertices=10, convex hull=31, v0=111314) After retessellation of defect 40 (v0=111314), euler #=-24 (176519,528797,352254) : difference with theory (-26) = -2 CORRECTING DEFECT 41 (vertices=52, convex hull=82, v0=113211) After retessellation of defect 41 (v0=113211), euler #=-24 (176541,528902,352337) : difference with theory (-25) = -1 CORRECTING DEFECT 42 (vertices=49, convex hull=23, v0=113314) After retessellation of defect 42 (v0=113314), euler #=-23 (176544,528916,352349) : difference with theory (-24) = -1 CORRECTING DEFECT 43 (vertices=10, convex hull=26, v0=118609) After retessellation of defect 43 (v0=118609), euler #=-22 (176547,528934,352365) : difference with theory (-23) = -1 CORRECTING DEFECT 44 (vertices=61, convex hull=79, v0=125606) After retessellation of defect 44 (v0=125606), euler #=-21 (176570,529035,352444) : difference with theory (-22) = -1 CORRECTING DEFECT 45 (vertices=31, convex hull=40, v0=128748) After retessellation of defect 45 (v0=128748), euler #=-20 (176578,529075,352477) : difference with theory (-21) = -1 CORRECTING DEFECT 46 (vertices=26, convex hull=31, v0=133046) After retessellation of defect 46 (v0=133046), euler #=-19 (176582,529096,352495) : difference with theory (-20) = -1 CORRECTING DEFECT 47 (vertices=852, convex hull=462, v0=136828) L defect detected... After retessellation of defect 47 (v0=136828), euler #=-19 (176803,530008,353186) : difference with theory (-19) = 0 CORRECTING DEFECT 48 (vertices=12, convex hull=25, v0=138014) After retessellation of defect 48 (v0=138014), euler #=-18 (176806,530025,353201) : difference with theory (-18) = 0 CORRECTING DEFECT 49 (vertices=25, convex hull=43, v0=138325) After retessellation of defect 49 (v0=138325), euler #=-17 (176813,530061,353231) : difference with theory (-17) = 0 CORRECTING DEFECT 50 (vertices=11, convex hull=28, v0=139944) After retessellation of defect 50 (v0=139944), euler #=-16 (176815,530078,353247) : difference with theory (-16) = 0 CORRECTING DEFECT 51 (vertices=11, convex hull=18, v0=140724) After retessellation of defect 51 (v0=140724), euler #=-15 (176817,530088,353256) : difference with theory (-15) = 0 CORRECTING DEFECT 52 (vertices=110, convex hull=125, v0=141947) After retessellation of defect 52 (v0=141947), euler #=-14 (176871,530309,353424) : difference with theory (-14) = 0 CORRECTING DEFECT 53 (vertices=6, convex hull=19, v0=143102) After retessellation of defect 53 (v0=143102), euler #=-13 (176873,530319,353433) : difference with theory (-13) = 0 CORRECTING DEFECT 54 (vertices=5, convex hull=14, v0=146226) After retessellation of defect 54 (v0=146226), euler #=-12 (176874,530326,353440) : difference with theory (-12) = 0 CORRECTING DEFECT 55 (vertices=38, convex hull=52, v0=146519) After retessellation of defect 55 (v0=146519), euler #=-11 (176885,530380,353484) : difference with theory (-11) = 0 CORRECTING DEFECT 56 (vertices=18, convex hull=57, v0=149838) After retessellation of defect 56 (v0=149838), euler #=-10 (176894,530428,353524) : difference with theory (-10) = 0 CORRECTING DEFECT 57 (vertices=62, convex hull=40, v0=150493) After retessellation of defect 57 (v0=150493), euler #=-9 (176902,530467,353556) : difference with theory (-9) = 0 CORRECTING DEFECT 58 (vertices=7, convex hull=29, v0=151561) After retessellation of defect 58 (v0=151561), euler #=-8 (176904,530483,353571) : difference with theory (-8) = 0 CORRECTING DEFECT 59 (vertices=58, convex hull=58, v0=154994) After retessellation of defect 59 (v0=154994), euler #=-7 (176937,530607,353663) : difference with theory (-7) = 0 CORRECTING DEFECT 60 (vertices=29, convex hull=71, v0=160466) After retessellation of defect 60 (v0=160466), euler #=-6 (176948,530671,353717) : difference with theory (-6) = 0 CORRECTING DEFECT 61 (vertices=36, convex hull=67, v0=162332) After retessellation of defect 61 (v0=162332), euler #=-5 (176957,530727,353765) : difference with theory (-5) = 0 CORRECTING DEFECT 62 (vertices=49, convex hull=71, v0=164576) After retessellation of defect 62 (v0=164576), euler #=-4 (176973,530802,353825) : difference with theory (-4) = 0 CORRECTING DEFECT 63 (vertices=46, convex hull=89, v0=166225) After retessellation of defect 63 (v0=166225), euler #=-3 (176993,530899,353903) : difference with theory (-3) = 0 CORRECTING DEFECT 64 (vertices=11, convex hull=24, v0=169267) After retessellation of defect 64 (v0=169267), euler #=-2 (176995,530911,353914) : difference with theory (-2) = 0 CORRECTING DEFECT 65 (vertices=33, convex hull=72, v0=169967) After retessellation of defect 65 (v0=169967), euler #=-1 (177011,530986,353974) : difference with theory (-1) = 0 CORRECTING DEFECT 66 (vertices=63, convex hull=37, v0=176344) After retessellation of defect 66 (v0=176344), euler #=0 (177015,531015,354000) : difference with theory (0) = 0 CORRECTING DEFECT 67 (vertices=6, convex hull=22, v0=181665) After retessellation of defect 67 (v0=181665), euler #=1 (177015,531023,354009) : difference with theory (1) = 0 CORRECTING DEFECT 68 (vertices=17, convex hull=47, v0=181884) After retessellation of defect 68 (v0=181884), euler #=2 (177022,531060,354040) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.04-->15.83) (max @ vno 10724 --> 30050) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.04-->15.83) (max @ vno 10724 --> 30050) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 221 mutations (35.8%), 396 crossovers (64.2%), 613 vertices were eliminated building final representation... 7410 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=177022, nf=354040, ne=531060, g=0) writing corrected surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 52.0 minutes 0 defective edges removing intersecting faces 000: 1120 intersecting 001: 86 intersecting 002: 48 intersecting expanding nbhd size to 2 003: 48 intersecting 004: 30 intersecting 005: 23 intersecting 006: 20 intersecting mris_fix_topology utimesec 3117.454991 mris_fix_topology stimesec 1.158855 mris_fix_topology ru_maxrss 602352 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 1137447 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 16792 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 447 mris_fix_topology ru_nivcsw 1698 FSRUNTIME@ mris_fix_topology lh 0.8664 hours 1 threads #@# Fix Topology rh Thu Sep 26 23:06:51 EDT 2019 mris_fix_topology -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 BIO-ALS-701-088-BL rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-160 (nv=185054, nf=370428, ne=555642, g=81) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 18084 ambiguous faces found in tessellation segmenting defects... 66 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 28 into 23 -merging segment 38 into 35 64 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9869 (-4.4934) -vertex loglikelihood: -5.9978 (-2.9989) -normal dot loglikelihood: -3.4859 (-3.4859) -quad curv loglikelihood: -6.2060 (-3.1030) Total Loglikelihood : -24.6765 CORRECTING DEFECT 0 (vertices=243, convex hull=161, v0=232) After retessellation of defect 0 (v0=232), euler #=-56 (174487,520164,345621) : difference with theory (-61) = -5 CORRECTING DEFECT 1 (vertices=69, convex hull=117, v0=714) After retessellation of defect 1 (v0=714), euler #=-55 (174503,520267,345709) : difference with theory (-60) = -5 CORRECTING DEFECT 2 (vertices=85, convex hull=128, v0=769) After retessellation of defect 2 (v0=769), euler #=-54 (174526,520396,345816) : difference with theory (-59) = -5 CORRECTING DEFECT 3 (vertices=223, convex hull=154, v0=1313) After retessellation of defect 3 (v0=1313), euler #=-53 (174544,520526,345929) : difference with theory (-58) = -5 CORRECTING DEFECT 4 (vertices=16, convex hull=31, v0=5341) After retessellation of defect 4 (v0=5341), euler #=-52 (174545,520540,345943) : difference with theory (-57) = -5 CORRECTING DEFECT 5 (vertices=71, convex hull=110, v0=5545) After retessellation of defect 5 (v0=5545), euler #=-51 (174569,520660,346040) : difference with theory (-56) = -5 CORRECTING DEFECT 6 (vertices=2945, convex hull=867, v0=10621) XL defect detected... After retessellation of defect 6 (v0=10621), euler #=-52 (174830,521893,347011) : difference with theory (-55) = -3 CORRECTING DEFECT 7 (vertices=65, convex hull=88, v0=13049) After retessellation of defect 7 (v0=13049), euler #=-51 (174865,522037,347121) : difference with theory (-54) = -3 CORRECTING DEFECT 8 (vertices=33, convex hull=77, v0=15173) After retessellation of defect 8 (v0=15173), euler #=-50 (174883,522119,347186) : difference with theory (-53) = -3 CORRECTING DEFECT 9 (vertices=59, convex hull=84, v0=15923) After retessellation of defect 9 (v0=15923), euler #=-49 (174908,522225,347268) : difference with theory (-52) = -3 CORRECTING DEFECT 10 (vertices=10, convex hull=33, v0=16968) After retessellation of defect 10 (v0=16968), euler #=-48 (174910,522243,347285) : difference with theory (-51) = -3 CORRECTING DEFECT 11 (vertices=34, convex hull=46, v0=23175) After retessellation of defect 11 (v0=23175), euler #=-47 (174916,522279,347316) : difference with theory (-50) = -3 CORRECTING DEFECT 12 (vertices=9, convex hull=27, v0=30803) After retessellation of defect 12 (v0=30803), euler #=-46 (174917,522291,347328) : difference with theory (-49) = -3 CORRECTING DEFECT 13 (vertices=31, convex hull=76, v0=38129) After retessellation of defect 13 (v0=38129), euler #=-45 (174933,522370,347392) : difference with theory (-48) = -3 CORRECTING DEFECT 14 (vertices=22, convex hull=45, v0=53843) After retessellation of defect 14 (v0=53843), euler #=-44 (174941,522409,347424) : difference with theory (-47) = -3 CORRECTING DEFECT 15 (vertices=22, convex hull=53, v0=56969) After retessellation of defect 15 (v0=56969), euler #=-43 (174949,522455,347463) : difference with theory (-46) = -3 CORRECTING DEFECT 16 (vertices=18, convex hull=29, v0=65724) After retessellation of defect 16 (v0=65724), euler #=-42 (174952,522473,347479) : difference with theory (-45) = -3 CORRECTING DEFECT 17 (vertices=82, convex hull=55, v0=73415) After retessellation of defect 17 (v0=73415), euler #=-41 (174970,522550,347539) : difference with theory (-44) = -3 CORRECTING DEFECT 18 (vertices=28, convex hull=47, v0=73958) After retessellation of defect 18 (v0=73958), euler #=-40 (174979,522596,347577) : difference with theory (-43) = -3 CORRECTING DEFECT 19 (vertices=255, convex hull=179, v0=75668) After retessellation of defect 19 (v0=75668), euler #=-40 (175097,523049,347912) : difference with theory (-42) = -2 CORRECTING DEFECT 20 (vertices=43, convex hull=29, v0=81527) After retessellation of defect 20 (v0=81527), euler #=-39 (175103,523075,347933) : difference with theory (-41) = -2 CORRECTING DEFECT 21 (vertices=547, convex hull=229, v0=83069) After retessellation of defect 21 (v0=83069), euler #=-38 (175253,523641,348350) : difference with theory (-40) = -2 CORRECTING DEFECT 22 (vertices=45, convex hull=80, v0=84743) After retessellation of defect 22 (v0=84743), euler #=-37 (175279,523754,348438) : difference with theory (-39) = -2 CORRECTING DEFECT 23 (vertices=1379, convex hull=1044, v0=86767) XL defect detected... After retessellation of defect 23 (v0=86767), euler #=-39 (175730,525691,349922) : difference with theory (-38) = 1 CORRECTING DEFECT 24 (vertices=44, convex hull=71, v0=88507) After retessellation of defect 24 (v0=88507), euler #=-38 (175747,525770,349985) : difference with theory (-37) = 1 CORRECTING DEFECT 25 (vertices=111, convex hull=121, v0=88986) After retessellation of defect 25 (v0=88986), euler #=-37 (175812,526020,350171) : difference with theory (-36) = 1 CORRECTING DEFECT 26 (vertices=1130, convex hull=705, v0=91737) XL defect detected... After retessellation of defect 26 (v0=91737), euler #=-36 (176295,527835,351504) : difference with theory (-35) = 1 CORRECTING DEFECT 27 (vertices=217, convex hull=209, v0=93458) After retessellation of defect 27 (v0=93458), euler #=-35 (176386,528201,351780) : difference with theory (-34) = 1 CORRECTING DEFECT 28 (vertices=34, convex hull=62, v0=111128) After retessellation of defect 28 (v0=111128), euler #=-34 (176405,528283,351844) : difference with theory (-33) = 1 CORRECTING DEFECT 29 (vertices=40, convex hull=60, v0=112435) After retessellation of defect 29 (v0=112435), euler #=-33 (176415,528335,351887) : difference with theory (-32) = 1 CORRECTING DEFECT 30 (vertices=21, convex hull=47, v0=112671) After retessellation of defect 30 (v0=112671), euler #=-32 (176423,528374,351919) : difference with theory (-31) = 1 CORRECTING DEFECT 31 (vertices=31, convex hull=32, v0=112951) After retessellation of defect 31 (v0=112951), euler #=-31 (176425,528388,351932) : difference with theory (-30) = 1 CORRECTING DEFECT 32 (vertices=266, convex hull=152, v0=117786) After retessellation of defect 32 (v0=117786), euler #=-30 (176500,528678,352148) : difference with theory (-29) = 1 CORRECTING DEFECT 33 (vertices=15, convex hull=18, v0=119645) After retessellation of defect 33 (v0=119645), euler #=-29 (176503,528690,352158) : difference with theory (-28) = 1 CORRECTING DEFECT 34 (vertices=65, convex hull=75, v0=120280) After retessellation of defect 34 (v0=120280), euler #=-27 (176515,528758,352216) : difference with theory (-27) = 0 CORRECTING DEFECT 35 (vertices=40, convex hull=49, v0=123792) After retessellation of defect 35 (v0=123792), euler #=-26 (176533,528829,352270) : difference with theory (-26) = 0 CORRECTING DEFECT 36 (vertices=40, convex hull=49, v0=125064) After retessellation of defect 36 (v0=125064), euler #=-25 (176546,528890,352319) : difference with theory (-25) = 0 CORRECTING DEFECT 37 (vertices=64, convex hull=70, v0=129001) After retessellation of defect 37 (v0=129001), euler #=-24 (176580,529026,352422) : difference with theory (-24) = 0 CORRECTING DEFECT 38 (vertices=6, convex hull=18, v0=129901) After retessellation of defect 38 (v0=129901), euler #=-23 (176582,529038,352433) : difference with theory (-23) = 0 CORRECTING DEFECT 39 (vertices=145, convex hull=133, v0=130389) After retessellation of defect 39 (v0=130389), euler #=-22 (176603,529163,352538) : difference with theory (-22) = 0 CORRECTING DEFECT 40 (vertices=72, convex hull=57, v0=131408) After retessellation of defect 40 (v0=131408), euler #=-21 (176625,529251,352605) : difference with theory (-21) = 0 CORRECTING DEFECT 41 (vertices=30, convex hull=72, v0=131569) After retessellation of defect 41 (v0=131569), euler #=-20 (176634,529306,352652) : difference with theory (-20) = 0 CORRECTING DEFECT 42 (vertices=147, convex hull=95, v0=132458) After retessellation of defect 42 (v0=132458), euler #=-19 (176660,529430,352751) : difference with theory (-19) = 0 CORRECTING DEFECT 43 (vertices=31, convex hull=28, v0=135010) After retessellation of defect 43 (v0=135010), euler #=-18 (176662,529445,352765) : difference with theory (-18) = 0 CORRECTING DEFECT 44 (vertices=20, convex hull=37, v0=137869) After retessellation of defect 44 (v0=137869), euler #=-17 (176670,529481,352794) : difference with theory (-17) = 0 CORRECTING DEFECT 45 (vertices=29, convex hull=23, v0=138453) After retessellation of defect 45 (v0=138453), euler #=-16 (176673,529496,352807) : difference with theory (-16) = 0 CORRECTING DEFECT 46 (vertices=237, convex hull=136, v0=138949) After retessellation of defect 46 (v0=138949), euler #=-15 (176798,529940,353127) : difference with theory (-15) = 0 CORRECTING DEFECT 47 (vertices=32, convex hull=29, v0=141309) After retessellation of defect 47 (v0=141309), euler #=-14 (176803,529966,353149) : difference with theory (-14) = 0 CORRECTING DEFECT 48 (vertices=467, convex hull=232, v0=143440) normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces normal vector of length zero at vertex 183773 with 3 faces After retessellation of defect 48 (v0=143440), euler #=-13 (176885,530316,353418) : difference with theory (-13) = 0 CORRECTING DEFECT 49 (vertices=17, convex hull=48, v0=143749) After retessellation of defect 49 (v0=143749), euler #=-12 (176893,530359,353454) : difference with theory (-12) = 0 CORRECTING DEFECT 50 (vertices=169, convex hull=59, v0=145030) After retessellation of defect 50 (v0=145030), euler #=-11 (176903,530417,353503) : difference with theory (-11) = 0 CORRECTING DEFECT 51 (vertices=21, convex hull=28, v0=146174) After retessellation of defect 51 (v0=146174), euler #=-10 (176908,530442,353524) : difference with theory (-10) = 0 CORRECTING DEFECT 52 (vertices=169, convex hull=70, v0=152181) After retessellation of defect 52 (v0=152181), euler #=-9 (176943,530580,353628) : difference with theory (-9) = 0 CORRECTING DEFECT 53 (vertices=31, convex hull=38, v0=153009) After retessellation of defect 53 (v0=153009), euler #=-8 (176951,530619,353660) : difference with theory (-8) = 0 CORRECTING DEFECT 54 (vertices=50, convex hull=39, v0=157751) After retessellation of defect 54 (v0=157751), euler #=-7 (176960,530659,353692) : difference with theory (-7) = 0 CORRECTING DEFECT 55 (vertices=16, convex hull=25, v0=157854) After retessellation of defect 55 (v0=157854), euler #=-6 (176963,530678,353709) : difference with theory (-6) = 0 CORRECTING DEFECT 56 (vertices=67, convex hull=49, v0=158248) After retessellation of defect 56 (v0=158248), euler #=-5 (176973,530727,353749) : difference with theory (-5) = 0 CORRECTING DEFECT 57 (vertices=35, convex hull=22, v0=158742) After retessellation of defect 57 (v0=158742), euler #=-4 (176974,530734,353756) : difference with theory (-4) = 0 CORRECTING DEFECT 58 (vertices=125, convex hull=71, v0=163894) After retessellation of defect 58 (v0=163894), euler #=-3 (176985,530794,353806) : difference with theory (-3) = 0 CORRECTING DEFECT 59 (vertices=28, convex hull=50, v0=180329) After retessellation of defect 59 (v0=180329), euler #=-2 (176992,530833,353839) : difference with theory (-2) = 0 CORRECTING DEFECT 60 (vertices=64, convex hull=75, v0=181258) After retessellation of defect 60 (v0=181258), euler #=-1 (177010,530921,353910) : difference with theory (-1) = 0 CORRECTING DEFECT 61 (vertices=65, convex hull=63, v0=181742) After retessellation of defect 61 (v0=181742), euler #=0 (177012,530951,353939) : difference with theory (0) = 0 CORRECTING DEFECT 62 (vertices=38, convex hull=66, v0=182112) After retessellation of defect 62 (v0=182112), euler #=1 (177022,531008,353987) : difference with theory (1) = 0 CORRECTING DEFECT 63 (vertices=62, convex hull=125, v0=183148) After retessellation of defect 63 (v0=183148), euler #=2 (177054,531156,354104) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.02-->16.66) (max @ vno 18807 --> 27458) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.02-->16.66) (max @ vno 18807 --> 27458) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 206 mutations (33.6%), 408 crossovers (66.4%), 1006 vertices were eliminated building final representation... 8000 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=177054, nf=354104, ne=531156, g=0) writing corrected surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 60.5 minutes 0 defective edges removing intersecting faces 000: 815 intersecting 001: 49 intersecting 002: 4 intersecting mris_fix_topology utimesec 3630.528077 mris_fix_topology stimesec 0.835893 mris_fix_topology ru_maxrss 606900 mris_fix_topology ru_ixrss 0 mris_fix_topology ru_idrss 0 mris_fix_topology ru_isrss 0 mris_fix_topology ru_minflt 662127 mris_fix_topology ru_majflt 0 mris_fix_topology ru_nswap 0 mris_fix_topology ru_inblock 0 mris_fix_topology ru_oublock 16800 mris_fix_topology ru_msgsnd 0 mris_fix_topology ru_msgrcv 0 mris_fix_topology ru_nsignals 0 mris_fix_topology ru_nvcsw 552 mris_fix_topology ru_nivcsw 1970 FSRUNTIME@ mris_fix_topology rh 1.0089 hours 1 threads mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 177022 - 531060 + 354040 = 2 --> 0 holes F =2V-4: 354040 = 354044-4 (0) 2E=3F: 1062120 = 1062120 (0) total defect index = 0 mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 177054 - 531156 + 354104 = 2 --> 0 holes F =2V-4: 354104 = 354108-4 (0) 2E=3F: 1062312 = 1062312 (0) total defect index = 0 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 489 intersecting 001: 74 intersecting 002: 45 intersecting expanding nbhd size to 2 003: 60 intersecting 004: 55 intersecting 005: 45 intersecting 006: 28 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 212 intersecting 001: 27 intersecting 002: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Sep 27 00:07:39 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs BIO-ALS-701-088-BL lh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/filled.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... 31503 bright wm thresholded. 4021 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.orig... computing class statistics... border white: 349585 voxels (2.08%) border gray 375151 voxels (2.24%) WM (98.0): 98.8 +- 7.1 [70.0 --> 110.0] GM (78.0) : 75.9 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.8 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.01-->6.12) (max @ vno 175715 --> 175765) face area 0.28 +- 0.14 (0.00-->7.61) mean absolute distance = 0.74 +- 1.00 4360 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=75+-7.0 mean inside = 95.0, mean outside = 79.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=85.1, 132 (132) missing vertices, mean dist 0.1 [0.7 (%39.6)->0.7 (%60.4))] %60 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.05-->7.97) (max @ vno 175712 --> 175715) face area 0.28 +- 0.14 (0.00-->7.09) mean absolute distance = 0.44 +- 0.73 7134 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3093831.5, rms=8.244 001: dt: 0.5000, sse=1835105.5, rms=5.747 (30.290%) 002: dt: 0.5000, sse=1303865.4, rms=4.206 (26.803%) 003: dt: 0.5000, sse=1094696.0, rms=3.372 (19.829%) 004: dt: 0.5000, sse=998833.3, rms=2.961 (12.184%) 005: dt: 0.5000, sse=968136.3, rms=2.800 (5.446%) 006: dt: 0.5000, sse=953537.3, rms=2.716 (3.012%) rms = 2.69, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=946576.6, rms=2.687 (1.045%) 008: dt: 0.2500, sse=831577.2, rms=1.843 (31.429%) 009: dt: 0.2500, sse=812612.4, rms=1.679 (8.886%) rms = 1.66, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=811850.4, rms=1.656 (1.343%) rms = 1.62, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=806999.7, rms=1.623 (1.991%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=87.4, 154 (43) missing vertices, mean dist -0.3 [0.5 (%66.1)->0.3 (%33.9))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.06-->8.19) (max @ vno 175712 --> 175715) face area 0.34 +- 0.18 (0.00-->9.38) mean absolute distance = 0.35 +- 0.50 7354 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1419475.5, rms=3.980 012: dt: 0.5000, sse=1117299.8, rms=2.623 (34.111%) 013: dt: 0.5000, sse=1063515.4, rms=2.330 (11.172%) rms = 2.29, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=1049366.8, rms=2.287 (1.832%) 015: dt: 0.2500, sse=976585.7, rms=1.674 (26.818%) 016: dt: 0.2500, sse=960140.4, rms=1.525 (8.874%) rms = 1.48, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=956164.0, rms=1.478 (3.109%) rms = 1.45, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=954682.9, rms=1.451 (1.839%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=89.3, 184 (31) missing vertices, mean dist -0.2 [0.4 (%67.4)->0.2 (%32.6))] %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.26 (0.05-->8.26) (max @ vno 175712 --> 175715) face area 0.33 +- 0.18 (0.00-->9.39) mean absolute distance = 0.29 +- 0.40 5494 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1170828.8, rms=3.024 019: dt: 0.5000, sse=1026834.6, rms=2.064 (31.767%) rms = 2.02, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=1012189.6, rms=2.021 (2.080%) 021: dt: 0.2500, sse=932721.1, rms=1.417 (29.872%) 022: dt: 0.2500, sse=924430.8, rms=1.317 (7.067%) rms = 1.30, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=925265.9, rms=1.299 (1.351%) rms = 1.27, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=925964.9, rms=1.273 (1.987%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.1, 215 (24) missing vertices, mean dist -0.1 [0.3 (%56.8)->0.2 (%43.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.preaparc... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=959158.7, rms=1.739 025: dt: 0.5000, sse=915994.4, rms=1.350 (22.334%) rms = 1.70, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=890146.4, rms=1.112 (17.691%) rms = 1.09, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=893395.1, rms=1.091 (1.823%) rms = 1.05, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=883132.7, rms=1.050 (3.748%) positioning took 0.4 minutes generating cortex label... 13 non-cortical segments detected only using segment with 7915 vertices erasing segment 0 (vno[0] = 66550) erasing segment 2 (vno[0] = 83782) erasing segment 3 (vno[0] = 103319) erasing segment 4 (vno[0] = 105516) erasing segment 5 (vno[0] = 131101) erasing segment 6 (vno[0] = 132440) erasing segment 7 (vno[0] = 133460) erasing segment 8 (vno[0] = 134545) erasing segment 9 (vno[0] = 135695) erasing segment 10 (vno[0] = 137545) erasing segment 11 (vno[0] = 150594) erasing segment 12 (vno[0] = 176592) writing cortex label to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label... writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area vertex spacing 0.88 +- 0.27 (0.01-->8.28) (max @ vno 175712 --> 175715) face area 0.33 +- 0.17 (0.00-->9.59) refinement took 4.2 minutes #-------------------------------------------- #@# Make White Surf rh Fri Sep 27 00:11:54 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs BIO-ALS-701-088-BL rh using white.preaparc as white matter name... only generating white matter surface using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/filled.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... 31503 bright wm thresholded. 4021 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.orig... computing class statistics... border white: 349585 voxels (2.08%) border gray 375151 voxels (2.24%) WM (98.0): 98.8 +- 7.1 [70.0 --> 110.0] GM (78.0) : 75.9 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 55.8 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.01-->5.38) (max @ vno 175139 --> 175243) face area 0.28 +- 0.13 (0.00-->6.78) mean absolute distance = 0.74 +- 1.03 4808 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=78+-7.8 mean inside = 95.1, mean outside = 80.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=86.7, 88 (88) missing vertices, mean dist 0.0 [0.8 (%44.7)->0.7 (%55.3))] %54 local maxima, %42 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.25 (0.04-->7.61) (max @ vno 175243 --> 175139) face area 0.28 +- 0.13 (0.00-->5.31) mean absolute distance = 0.43 +- 0.73 6730 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3068180.2, rms=8.238 001: dt: 0.5000, sse=1791816.6, rms=5.637 (31.574%) 002: dt: 0.5000, sse=1270938.9, rms=4.066 (27.878%) 003: dt: 0.5000, sse=1068224.2, rms=3.277 (19.393%) 004: dt: 0.5000, sse=992471.3, rms=2.875 (12.271%) 005: dt: 0.5000, sse=945891.5, rms=2.684 (6.655%) 006: dt: 0.5000, sse=935474.4, rms=2.575 (4.038%) rms = 2.54, time step reduction 1 of 3 to 0.250... 007: dt: 0.5000, sse=922291.3, rms=2.544 (1.212%) 008: dt: 0.2500, sse=817460.2, rms=1.714 (32.632%) 009: dt: 0.2500, sse=799617.2, rms=1.551 (9.529%) rms = 1.51, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=800915.8, rms=1.511 (2.567%) rms = 1.48, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=793061.3, rms=1.478 (2.194%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... mean border=88.9, 153 (29) missing vertices, mean dist -0.3 [0.5 (%65.6)->0.2 (%34.4))] %66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.04-->8.13) (max @ vno 175243 --> 175139) face area 0.34 +- 0.17 (0.00-->6.82) mean absolute distance = 0.34 +- 0.51 6378 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1330919.0, rms=3.680 012: dt: 0.5000, sse=1065064.5, rms=2.391 (35.026%) 013: dt: 0.5000, sse=1021292.8, rms=2.124 (11.160%) rms = 2.12, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=1018653.2, rms=2.115 (0.417%) 015: dt: 0.2500, sse=950009.9, rms=1.507 (28.740%) 016: dt: 0.2500, sse=942078.8, rms=1.386 (8.082%) rms = 1.36, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=941094.6, rms=1.360 (1.846%) rms = 1.33, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=930312.2, rms=1.329 (2.276%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=90.7, 142 (19) missing vertices, mean dist -0.2 [0.4 (%66.2)->0.2 (%33.8))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.25 (0.05-->8.51) (max @ vno 175243 --> 175139) face area 0.33 +- 0.17 (0.00-->7.01) mean absolute distance = 0.29 +- 0.41 5816 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1112972.4, rms=2.783 019: dt: 0.5000, sse=991423.4, rms=1.899 (31.785%) rms = 1.86, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=975394.9, rms=1.862 (1.920%) 021: dt: 0.2500, sse=953853.7, rms=1.338 (28.147%) 022: dt: 0.2500, sse=909084.4, rms=1.243 (7.089%) rms = 1.24, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=911033.2, rms=1.235 (0.644%) rms = 1.21, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=902149.7, rms=1.209 (2.117%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=91.5, 189 (15) missing vertices, mean dist -0.1 [0.3 (%56.0)->0.2 (%44.0))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.preaparc... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=930728.7, rms=1.636 025: dt: 0.5000, sse=906124.2, rms=1.267 (22.542%) rms = 1.60, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=878753.8, rms=1.045 (17.545%) rms = 1.03, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=877325.8, rms=1.027 (1.689%) rms = 0.98, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=874092.4, rms=0.985 (4.143%) positioning took 0.5 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8110 vertices erasing segment 1 (vno[0] = 91774) erasing segment 2 (vno[0] = 93812) erasing segment 3 (vno[0] = 104718) erasing segment 4 (vno[0] = 123177) erasing segment 5 (vno[0] = 129007) erasing segment 6 (vno[0] = 132395) erasing segment 7 (vno[0] = 140402) erasing segment 8 (vno[0] = 175752) writing cortex label to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label... writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area vertex spacing 0.88 +- 0.26 (0.01-->8.65) (max @ vno 175139 --> 175243) face area 0.33 +- 0.17 (0.00-->6.88) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 lh Fri Sep 27 00:16:08 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth2 rh Fri Sep 27 00:16:14 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Fri Sep 27 00:16:19 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_inflate -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 52.2 mm, total surface area = 104555 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.178 (target=0.015) step 005: RMS=0.127 (target=0.015) step 010: RMS=0.096 (target=0.015) step 015: RMS=0.079 (target=0.015) step 020: RMS=0.066 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.040 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.031 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.024 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.471650 mris_inflate stimesec 0.169989 mris_inflate ru_maxrss 226684 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 166450 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13840 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 341 mris_inflate ru_nivcsw 12 #-------------------------------------------- #@# Inflation2 rh Fri Sep 27 00:16:56 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_inflate -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 52.3 mm, total surface area = 104184 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.177 (target=0.015) step 005: RMS=0.126 (target=0.015) step 010: RMS=0.095 (target=0.015) step 015: RMS=0.077 (target=0.015) step 020: RMS=0.064 (target=0.015) step 025: RMS=0.054 (target=0.015) step 030: RMS=0.046 (target=0.015) step 035: RMS=0.039 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.6 minutes mris_inflate utimesec 36.100981 mris_inflate stimesec 0.151987 mris_inflate ru_maxrss 226400 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 145243 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 13840 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 562 mris_inflate ru_nivcsw 12 #-------------------------------------------- #@# Curv .H and .K lh Fri Sep 27 00:17:33 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_curvature -w lh.white.preaparc total integrated curvature = 22.664*4pi (284.799) --> -22 handles ICI = 254.5, FI = 2254.8, variation=36611.834 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 238 vertices thresholded to be in k1 ~ [-0.21 0.48], k2 ~ [-0.09 0.06] total integrated curvature = 0.483*4pi (6.070) --> 1 handles ICI = 1.6, FI = 11.0, variation=184.662 170 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 172 vertices thresholded to be in [-0.12 0.23] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.014, std = 0.022 done. #-------------------------------------------- #@# Curv .H and .K rh Fri Sep 27 00:18:47 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_curvature -w rh.white.preaparc total integrated curvature = 17.840*4pi (224.181) --> -17 handles ICI = 249.4, FI = 2238.8, variation=36315.503 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 256 vertices thresholded to be in k1 ~ [-0.28 0.61], k2 ~ [-0.09 0.07] total integrated curvature = 0.427*4pi (5.360) --> 1 handles ICI = 1.6, FI = 12.8, variation=210.467 161 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 168 vertices thresholded to be in [-0.15 0.24] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.014, std = 0.025 done. #----------------------------------------- #@# Curvature Stats lh Fri Sep 27 00:20:02 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm BIO-ALS-701-088-BL lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ BIO-ALS-701-088-BL/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 346 ] Gb_filter = 0 WARN: S lookup min: -0.165699 WARN: S explicit min: 0.000000 vertex = 61 #----------------------------------------- #@# Curvature Stats rh Fri Sep 27 00:20:06 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm BIO-ALS-701-088-BL rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ BIO-ALS-701-088-BL/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 359 ] Gb_filter = 0 WARN: S lookup min: -0.372845 WARN: S explicit min: 0.000000 vertex = 765 #-------------------------------------------- #@# Sphere lh Fri Sep 27 00:20:10 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_sphere -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.270... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.13 pass 1: epoch 2 of 3 starting distance error %20.15 unfolding complete - removing small folds... starting distance error %20.11 removing remaining folds... final distance error %20.13 MRISunfold() return, current seed 1234 -01: dt=0.0000, 408 negative triangles 243: dt=0.9900, 408 negative triangles 244: dt=0.9900, 253 negative triangles 245: dt=0.9900, 219 negative triangles 246: dt=0.9900, 197 negative triangles 247: dt=0.9900, 186 negative triangles 248: dt=0.9900, 175 negative triangles 249: dt=0.9900, 185 negative triangles 250: dt=0.9900, 167 negative triangles 251: dt=0.9900, 170 negative triangles 252: dt=0.9900, 164 negative triangles 253: dt=0.9900, 165 negative triangles 254: dt=0.9900, 153 negative triangles 255: dt=0.9900, 150 negative triangles 256: dt=0.9900, 141 negative triangles 257: dt=0.9900, 147 negative triangles 258: dt=0.9900, 144 negative triangles 259: dt=0.9900, 128 negative triangles 260: dt=0.9900, 127 negative triangles 261: dt=0.9900, 122 negative triangles 262: dt=0.9900, 123 negative triangles 263: dt=0.9900, 98 negative triangles 264: dt=0.9900, 101 negative triangles 265: dt=0.9900, 112 negative triangles 266: dt=0.9900, 95 negative triangles 267: dt=0.9900, 84 negative triangles 268: dt=0.9900, 79 negative triangles 269: dt=0.9900, 82 negative triangles 270: dt=0.9900, 84 negative triangles 271: dt=0.9900, 82 negative triangles 272: dt=0.9900, 70 negative triangles 273: dt=0.9900, 55 negative triangles 274: dt=0.9900, 53 negative triangles 275: dt=0.9900, 60 negative triangles 276: dt=0.9900, 53 negative triangles 277: dt=0.9900, 48 negative triangles 278: dt=0.9900, 37 negative triangles 279: dt=0.9900, 29 negative triangles 280: dt=0.9900, 30 negative triangles 281: dt=0.9900, 27 negative triangles 282: dt=0.9900, 28 negative triangles 283: dt=0.9900, 27 negative triangles 284: dt=0.9900, 22 negative triangles 285: dt=0.9900, 27 negative triangles 286: dt=0.9900, 21 negative triangles 287: dt=0.9900, 22 negative triangles 288: dt=0.9900, 19 negative triangles 289: dt=0.9900, 22 negative triangles 290: dt=0.9900, 15 negative triangles 291: dt=0.9900, 14 negative triangles 292: dt=0.9900, 13 negative triangles 293: dt=0.9900, 14 negative triangles 294: dt=0.9900, 16 negative triangles 295: dt=0.9900, 14 negative triangles 296: dt=0.9900, 11 negative triangles 297: dt=0.9900, 11 negative triangles 298: dt=0.9900, 10 negative triangles 299: dt=0.9900, 7 negative triangles 300: dt=0.9900, 9 negative triangles 301: dt=0.9900, 8 negative triangles 302: dt=0.9900, 6 negative triangles 303: dt=0.9900, 9 negative triangles 304: dt=0.9900, 7 negative triangles 305: dt=0.9900, 8 negative triangles 306: dt=0.9900, 6 negative triangles 307: dt=0.9900, 9 negative triangles 308: dt=0.9900, 5 negative triangles 309: dt=0.9900, 3 negative triangles 310: dt=0.9900, 3 negative triangles 311: dt=0.9900, 1 negative triangles 312: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.97 hours mris_sphere utimesec 3505.544190 mris_sphere stimesec 1.060879 mris_sphere ru_maxrss 312048 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1280415 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12456 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 320 mris_sphere ru_nivcsw 897 FSRUNTIME@ mris_sphere 0.9742 hours 1 threads #-------------------------------------------- #@# Sphere rh Fri Sep 27 01:18:37 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_sphere -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.273... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.51 pass 1: epoch 2 of 3 starting distance error %20.41 unfolding complete - removing small folds... starting distance error %20.31 removing remaining folds... final distance error %20.32 MRISunfold() return, current seed 1234 -01: dt=0.0000, 330 negative triangles 182: dt=0.9900, 330 negative triangles 183: dt=0.9900, 206 negative triangles 184: dt=0.9900, 169 negative triangles 185: dt=0.9900, 147 negative triangles 186: dt=0.9900, 122 negative triangles 187: dt=0.9900, 122 negative triangles 188: dt=0.9900, 112 negative triangles 189: dt=0.9900, 105 negative triangles 190: dt=0.9900, 96 negative triangles 191: dt=0.9900, 90 negative triangles 192: dt=0.9900, 79 negative triangles 193: dt=0.9900, 68 negative triangles 194: dt=0.9900, 63 negative triangles 195: dt=0.9900, 59 negative triangles 196: dt=0.9900, 57 negative triangles 197: dt=0.9900, 49 negative triangles 198: dt=0.9900, 43 negative triangles 199: dt=0.9900, 48 negative triangles 200: dt=0.9900, 35 negative triangles 201: dt=0.9900, 34 negative triangles 202: dt=0.9900, 38 negative triangles 203: dt=0.9900, 29 negative triangles 204: dt=0.9900, 33 negative triangles 205: dt=0.9900, 35 negative triangles 206: dt=0.9900, 31 negative triangles 207: dt=0.9900, 26 negative triangles 208: dt=0.9900, 26 negative triangles 209: dt=0.9900, 24 negative triangles 210: dt=0.9900, 24 negative triangles 211: dt=0.9900, 20 negative triangles 212: dt=0.9900, 26 negative triangles 213: dt=0.9900, 23 negative triangles 214: dt=0.9900, 18 negative triangles 215: dt=0.9900, 12 negative triangles 216: dt=0.9900, 16 negative triangles 217: dt=0.9900, 13 negative triangles 218: dt=0.9900, 16 negative triangles 219: dt=0.9900, 13 negative triangles 220: dt=0.9900, 15 negative triangles 221: dt=0.9900, 12 negative triangles 222: dt=0.9900, 11 negative triangles 223: dt=0.9900, 10 negative triangles 224: dt=0.9900, 10 negative triangles 225: dt=0.9900, 7 negative triangles 226: dt=0.9900, 12 negative triangles 227: dt=0.9900, 7 negative triangles 228: dt=0.9900, 10 negative triangles 229: dt=0.9900, 6 negative triangles 230: dt=0.9900, 8 negative triangles 231: dt=0.9900, 6 negative triangles 232: dt=0.9900, 10 negative triangles 233: dt=0.9900, 7 negative triangles 234: dt=0.9900, 5 negative triangles 235: dt=0.9900, 5 negative triangles 236: dt=0.9900, 8 negative triangles 237: dt=0.9900, 6 negative triangles 238: dt=0.9900, 4 negative triangles 239: dt=0.9900, 6 negative triangles 240: dt=0.9900, 4 negative triangles 241: dt=0.9900, 4 negative triangles 242: dt=0.9900, 6 negative triangles 243: dt=0.9900, 3 negative triangles 244: dt=0.9900, 1 negative triangles 245: dt=0.9900, 2 negative triangles 246: dt=0.9900, 1 negative triangles 247: dt=0.9900, 1 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.88 hours mris_sphere utimesec 3174.505311 mris_sphere stimesec 1.341825 mris_sphere ru_maxrss 311804 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 1402914 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 12456 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 465 mris_sphere ru_nivcsw 1171 FSRUNTIME@ mris_sphere 0.8823 hours 1 threads #-------------------------------------------- #@# Surf Reg lh Fri Sep 27 02:11:34 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_register -curv -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts cmdline mris_register -curv -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 5.471 curvature mean = 0.036, std = 0.822 curvature mean = 0.026, std = 0.832 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, -16.00) sse = 434791.2, tmin=0.9437 d=32.00 min @ (0.00, -8.00, 0.00) sse = 387810.2, tmin=1.8917 d=8.00 min @ (2.00, 2.00, -2.00) sse = 377864.0, tmin=3.7971 d=4.00 min @ (0.00, 1.00, 1.00) sse = 376967.6, tmin=4.7580 d=2.00 min @ (-0.50, -0.50, -0.50) sse = 376233.1, tmin=5.7192 d=1.00 min @ (0.00, 0.00, 0.25) sse = 376181.8, tmin=6.6803 d=0.50 min @ (0.00, 0.12, -0.12) sse = 376177.1, tmin=7.6428 tol=1.0e+00, sigma=0.5, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.64 min curvature mean = -0.011, std = 0.822 curvature mean = 0.009, std = 0.933 curvature mean = -0.021, std = 0.825 curvature mean = 0.004, std = 0.972 curvature mean = -0.024, std = 0.824 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.029, std = 0.305 curvature mean = 0.035, std = 0.244 curvature mean = 0.064, std = 0.310 curvature mean = 0.031, std = 0.300 curvature mean = 0.036, std = 0.490 curvature mean = 0.030, std = 0.326 curvature mean = 0.021, std = 0.628 curvature mean = 0.030, std = 0.336 curvature mean = 0.007, std = 0.740 MRISregister() return, current seed 0 -01: dt=0.0000, 218 negative triangles 137: dt=0.9900, 218 negative triangles expanding nbhd size to 1 138: dt=0.9900, 241 negative triangles 139: dt=0.9900, 222 negative triangles 140: dt=0.9900, 203 negative triangles 141: dt=0.9900, 200 negative triangles 142: dt=0.9900, 198 negative triangles 143: dt=0.9900, 194 negative triangles 144: dt=0.9900, 200 negative triangles 145: dt=0.9900, 204 negative triangles 146: dt=0.9900, 195 negative triangles 147: dt=0.9900, 197 negative triangles 148: dt=0.9900, 180 negative triangles 149: dt=0.9900, 187 negative triangles 150: dt=0.9900, 174 negative triangles 151: dt=0.9900, 178 negative triangles 152: dt=0.9900, 175 negative triangles 153: dt=0.9900, 164 negative triangles 154: dt=0.9900, 158 negative triangles 155: dt=0.9900, 165 negative triangles 156: dt=0.9900, 167 negative triangles 157: dt=0.9900, 162 negative triangles 158: dt=0.9900, 143 negative triangles 159: dt=0.9900, 145 negative triangles 160: dt=0.9900, 134 negative triangles 161: dt=0.9900, 131 negative triangles 162: dt=0.9900, 127 negative triangles 163: dt=0.9900, 123 negative triangles 164: dt=0.9900, 120 negative triangles 165: dt=0.9900, 114 negative triangles 166: dt=0.9900, 104 negative triangles 167: dt=0.9900, 106 negative triangles 168: dt=0.9900, 103 negative triangles 169: dt=0.9900, 93 negative triangles 170: dt=0.9900, 85 negative triangles 171: dt=0.9900, 87 negative triangles 172: dt=0.9900, 77 negative triangles 173: dt=0.9900, 82 negative triangles 174: dt=0.9900, 76 negative triangles 175: dt=0.9900, 67 negative triangles 176: dt=0.9900, 62 negative triangles 177: dt=0.9900, 61 negative triangles 178: dt=0.9900, 52 negative triangles 179: dt=0.9900, 54 negative triangles 180: dt=0.9900, 52 negative triangles 181: dt=0.9900, 49 negative triangles 182: dt=0.9900, 44 negative triangles 183: dt=0.9900, 39 negative triangles 184: dt=0.9900, 39 negative triangles 185: dt=0.9900, 29 negative triangles 186: dt=0.9900, 28 negative triangles 187: dt=0.9900, 32 negative triangles 188: dt=0.9900, 28 negative triangles 189: dt=0.9900, 24 negative triangles 190: dt=0.9900, 19 negative triangles 191: dt=0.9900, 28 negative triangles 192: dt=0.9900, 24 negative triangles 193: dt=0.9900, 21 negative triangles 194: dt=0.9900, 16 negative triangles 195: dt=0.9900, 17 negative triangles 196: dt=0.9900, 20 negative triangles 197: dt=0.9900, 16 negative triangles 198: dt=0.9900, 16 negative triangles 199: dt=0.9900, 16 negative triangles 200: dt=0.9900, 13 negative triangles 201: dt=0.9900, 13 negative triangles 202: dt=0.9900, 13 negative triangles 203: dt=0.9900, 11 negative triangles 204: dt=0.9900, 12 negative triangles 205: dt=0.9900, 8 negative triangles 206: dt=0.9900, 8 negative triangles 207: dt=0.9900, 7 negative triangles 208: dt=0.9900, 9 negative triangles 209: dt=0.9900, 6 negative triangles 210: dt=0.9900, 6 negative triangles 211: dt=0.9900, 3 negative triangles 212: dt=0.9900, 2 negative triangles 213: dt=0.9900, 2 negative triangles 214: dt=0.9900, 3 negative triangles 215: dt=0.9900, 1 negative triangles 216: dt=0.9900, 4 negative triangles writing registered surface to ../surf/lh.sphere.reg... registration took 1.47 hours mris_register utimesec 5272.708520 mris_register stimesec 0.709909 mris_register ru_maxrss 278908 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 239819 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 12456 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 221 mris_register ru_nivcsw 2190 FSRUNTIME@ mris_register 1.4650 hours 1 threads #-------------------------------------------- #@# Surf Reg rh Fri Sep 27 03:39:28 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_register -curv -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts cmdline mris_register -curv -rusage /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 5.488 curvature mean = 0.035, std = 0.817 curvature mean = 0.031, std = 0.835 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, -16.00, -16.00) sse = 484139.5, tmin=0.9788 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 419768.9, tmin=1.9365 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 419715.2, tmin=4.7983 d=2.00 min @ (0.50, 0.00, 0.00) sse = 419394.0, tmin=5.7613 d=1.00 min @ (0.00, 0.00, 0.25) sse = 419292.8, tmin=6.7283 d=0.50 min @ (0.12, 0.12, 0.00) sse = 419262.8, tmin=7.6998 tol=1.0e+00, sigma=0.5, host=aura., nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 7.70 min curvature mean = 0.001, std = 0.812 curvature mean = 0.011, std = 0.934 curvature mean = -0.010, std = 0.811 curvature mean = 0.004, std = 0.971 curvature mean = -0.015, std = 0.808 curvature mean = 0.001, std = 0.988 2 Reading smoothwm curvature mean = -0.032, std = 0.353 curvature mean = 0.032, std = 0.233 curvature mean = 0.062, std = 0.267 curvature mean = 0.026, std = 0.291 curvature mean = 0.035, std = 0.422 curvature mean = 0.024, std = 0.319 curvature mean = 0.019, std = 0.547 curvature mean = 0.024, std = 0.331 curvature mean = 0.007, std = 0.652 MRISregister() return, current seed 0 -01: dt=0.0000, 102 negative triangles 136: dt=0.9900, 102 negative triangles expanding nbhd size to 1 137: dt=0.9900, 111 negative triangles 138: dt=0.9900, 85 negative triangles 139: dt=0.9900, 74 negative triangles 140: dt=0.9900, 70 negative triangles 141: dt=0.9900, 69 negative triangles 142: dt=0.9900, 64 negative triangles 143: dt=0.9900, 65 negative triangles 144: dt=0.9900, 61 negative triangles 145: dt=0.9900, 52 negative triangles 146: dt=0.9900, 48 negative triangles 147: dt=0.9900, 46 negative triangles 148: dt=0.9900, 41 negative triangles 149: dt=0.9900, 35 negative triangles 150: dt=0.9900, 35 negative triangles 151: dt=0.9900, 34 negative triangles 152: dt=0.9900, 31 negative triangles 153: dt=0.9900, 31 negative triangles 154: dt=0.9900, 26 negative triangles 155: dt=0.9900, 25 negative triangles 156: dt=0.9900, 19 negative triangles 157: dt=0.9900, 17 negative triangles 158: dt=0.9900, 16 negative triangles 159: dt=0.9900, 16 negative triangles 160: dt=0.9900, 13 negative triangles 161: dt=0.9900, 12 negative triangles 162: dt=0.9900, 10 negative triangles 163: dt=0.9900, 12 negative triangles 164: dt=0.9900, 10 negative triangles 165: dt=0.9900, 9 negative triangles 166: dt=0.9900, 9 negative triangles 167: dt=0.9900, 9 negative triangles 168: dt=0.9900, 8 negative triangles 169: dt=0.9900, 8 negative triangles 170: dt=0.9900, 6 negative triangles 171: dt=0.9900, 6 negative triangles 172: dt=0.9900, 7 negative triangles 173: dt=0.9900, 5 negative triangles 174: dt=0.9900, 5 negative triangles 175: dt=0.9900, 5 negative triangles 176: dt=0.9900, 4 negative triangles 177: dt=0.9900, 4 negative triangles 178: dt=0.9900, 4 negative triangles 179: dt=0.9900, 4 negative triangles 180: dt=0.9900, 4 negative triangles 181: dt=0.9900, 4 negative triangles 182: dt=0.9900, 5 negative triangles 183: dt=0.9900, 5 negative triangles 184: dt=0.9900, 4 negative triangles 185: dt=0.9900, 4 negative triangles 186: dt=0.9405, 4 negative triangles 187: dt=0.9405, 4 negative triangles 188: dt=0.9405, 4 negative triangles 189: dt=0.9405, 4 negative triangles 190: dt=0.9405, 4 negative triangles 191: dt=0.9405, 4 negative triangles 192: dt=0.9405, 4 negative triangles 193: dt=0.9405, 4 negative triangles 194: dt=0.9405, 4 negative triangles 195: dt=0.9405, 3 negative triangles 196: dt=0.9405, 3 negative triangles 197: dt=0.9405, 3 negative triangles 198: dt=0.9405, 3 negative triangles 199: dt=0.9405, 3 negative triangles 200: dt=0.9405, 3 negative triangles 201: dt=0.9405, 2 negative triangles 202: dt=0.9405, 2 negative triangles 203: dt=0.9405, 2 negative triangles 204: dt=0.9405, 2 negative triangles 205: dt=0.9405, 1 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 1.32 hours mris_register utimesec 4750.814709 mris_register stimesec 0.896878 mris_register ru_maxrss 279684 mris_register ru_ixrss 0 mris_register ru_idrss 0 mris_register ru_isrss 0 mris_register ru_minflt 553298 mris_register ru_majflt 0 mris_register ru_nswap 0 mris_register ru_inblock 0 mris_register ru_oublock 12456 mris_register ru_msgsnd 0 mris_register ru_msgrcv 0 mris_register ru_nsignals 0 mris_register ru_nvcsw 394 mris_register ru_nivcsw 4667 FSRUNTIME@ mris_register 1.3201 hours 1 threads #-------------------------------------------- #@# Jacobian white lh Fri Sep 27 04:58:41 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# Jacobian white rh Fri Sep 27 04:58:43 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Fri Sep 27 04:58:45 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mrisp_paint -a 5 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... #-------------------------------------------- #@# AvgCurv rh Fri Sep 27 04:58:46 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mrisp_paint -a 5 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Sep 27 04:58:48 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL lh ../surf/lh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1386 labels changed using aseg relabeling using gibbs priors... 000: 3766 changed, 177022 examined... 001: 915 changed, 15782 examined... 002: 270 changed, 4994 examined... 003: 82 changed, 1548 examined... 004: 25 changed, 507 examined... 005: 12 changed, 158 examined... 006: 4 changed, 66 examined... 007: 2 changed, 20 examined... 008: 2 changed, 13 examined... 009: 2 changed, 13 examined... 010: 1 changed, 13 examined... 011: 0 changed, 7 examined... 242 labels changed using aseg 000: 142 total segments, 99 labels (423 vertices) changed 001: 46 total segments, 3 labels (4 vertices) changed 002: 42 total segments, 2 labels (5 vertices) changed 003: 40 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 10 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 2541 vertices marked for relabeling... 2541 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Cortical Parc rh Fri Sep 27 04:59:02 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL rh ../surf/rh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1062 labels changed using aseg relabeling using gibbs priors... 000: 3522 changed, 177054 examined... 001: 892 changed, 14999 examined... 002: 238 changed, 4937 examined... 003: 102 changed, 1423 examined... 004: 41 changed, 585 examined... 005: 17 changed, 233 examined... 006: 8 changed, 113 examined... 007: 8 changed, 48 examined... 008: 5 changed, 46 examined... 009: 2 changed, 27 examined... 010: 1 changed, 11 examined... 011: 0 changed, 7 examined... 216 labels changed using aseg 000: 119 total segments, 77 labels (332 vertices) changed 001: 45 total segments, 3 labels (9 vertices) changed 002: 42 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 3 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1974 vertices marked for relabeling... 1974 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 13 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Sep 27 04:59:15 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs BIO-ALS-701-088-BL lh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/filled.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... 31503 bright wm thresholded. 4021 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.orig... computing class statistics... border white: 349585 voxels (2.08%) border gray 375151 voxels (2.24%) WM (98.0): 98.8 +- 7.1 [70.0 --> 110.0] GM (78.0) : 75.9 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.8 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=75+-7.0 mean inside = 95.0, mean outside = 79.9 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.27 (0.01-->8.28) (max @ vno 175712 --> 175715) face area 0.33 +- 0.17 (0.00-->9.54) mean absolute distance = 0.70 +- 0.95 3808 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 6 points - only 0.00% unknown deleting segment 4 with 65 points - only 0.00% unknown deleting segment 5 with 10 points - only 0.00% unknown deleting segment 6 with 24 points - only 0.00% unknown deleting segment 7 with 7 points - only 0.00% unknown deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 73 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 19 points - only 0.00% unknown mean border=85.1, 237 (234) missing vertices, mean dist 0.4 [1.0 (%16.6)->0.6 (%83.4))] %59 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.05-->8.27) (max @ vno 75263 --> 78976) face area 0.33 +- 0.17 (0.00-->9.10) mean absolute distance = 0.42 +- 0.70 6143 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2347568.0, rms=6.653 001: dt: 0.5000, sse=1417960.5, rms=4.129 (37.939%) 002: dt: 0.5000, sse=1149564.8, rms=2.968 (28.112%) 003: dt: 0.5000, sse=1062154.5, rms=2.622 (11.676%) 004: dt: 0.5000, sse=1033877.7, rms=2.452 (6.469%) rms = 2.48, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=966543.8, rms=1.967 (19.788%) 006: dt: 0.2500, sse=945751.5, rms=1.715 (12.792%) 007: dt: 0.2500, sse=931009.8, rms=1.641 (4.310%) rms = 1.60, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=927510.2, rms=1.603 (2.320%) rms = 1.57, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=924363.5, rms=1.570 (2.060%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 11 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 2 with 70 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown deleting segment 4 with 8 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 5 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown deleting segment 7 with 31 points - only 48.39% unknown deleting segment 8 with 8 points - only 0.00% unknown deleting segment 9 with 8 points - only 0.00% unknown deleting segment 10 with 6 points - only 0.00% unknown deleting segment 11 with 5 points - only 0.00% unknown deleting segment 12 with 12 points - only 0.00% unknown mean border=87.4, 149 (58) missing vertices, mean dist -0.3 [0.5 (%65.4)->0.2 (%34.6))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.26 (0.05-->8.38) (max @ vno 175712 --> 175715) face area 0.34 +- 0.18 (0.00-->10.15) mean absolute distance = 0.35 +- 0.50 7187 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1373382.0, rms=3.783 010: dt: 0.5000, sse=1094972.4, rms=2.464 (34.878%) 011: dt: 0.5000, sse=1041754.4, rms=2.150 (12.719%) rms = 2.15, time step reduction 1 of 3 to 0.250... 012: dt: 0.5000, sse=1039081.9, rms=2.148 (0.107%) 013: dt: 0.2500, sse=965939.7, rms=1.498 (30.261%) 014: dt: 0.2500, sse=953823.4, rms=1.377 (8.078%) rms = 1.36, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=963111.8, rms=1.358 (1.375%) rms = 1.33, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=947666.5, rms=1.333 (1.828%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 12 points - only 0.00% unknown deleting segment 1 with 73 points - only 0.00% unknown deleting segment 2 with 16 points - only 0.00% unknown deleting segment 3 with 8 points - only 0.00% unknown deleting segment 5 with 20 points - only 0.00% unknown deleting segment 6 with 13 points - only 0.00% unknown deleting segment 7 with 14 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 12 points - only 0.00% unknown mean border=89.3, 173 (42) missing vertices, mean dist -0.2 [0.4 (%67.2)->0.2 (%32.8))] %82 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.05-->8.31) (max @ vno 175712 --> 175715) face area 0.33 +- 0.18 (0.00-->9.95) mean absolute distance = 0.29 +- 0.40 5426 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1160954.5, rms=2.970 017: dt: 0.5000, sse=1016157.8, rms=2.008 (32.397%) rms = 1.96, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=997206.2, rms=1.958 (2.482%) 019: dt: 0.2500, sse=931243.9, rms=1.365 (30.261%) 020: dt: 0.2500, sse=929861.7, rms=1.269 (7.067%) rms = 1.26, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=920210.2, rms=1.261 (0.633%) rms = 1.24, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=916676.1, rms=1.235 (2.005%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group deleting segment 0 with 2 points - only 0.00% unknown deleting segment 1 with 11 points - only 0.00% unknown deleting segment 2 with 71 points - only 0.00% unknown deleting segment 3 with 9 points - only 0.00% unknown deleting segment 4 with 17 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 20 points - only 0.00% unknown deleting segment 7 with 15 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 27 points - only 11.11% unknown deleting segment 13 with 12 points - only 0.00% unknown removing 1 vertex label from ripped group mean border=90.1, 201 (37) missing vertices, mean dist -0.1 [0.3 (%57.0)->0.2 (%43.0))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=949857.6, rms=1.715 023: dt: 0.5000, sse=923824.9, rms=1.330 (22.453%) rms = 1.68, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=892029.4, rms=1.084 (18.518%) rms = 1.06, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=894553.7, rms=1.056 (2.543%) rms = 1.02, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=886398.8, rms=1.021 (3.364%) positioning took 0.4 minutes generating cortex label... 15 non-cortical segments detected only using segment with 7892 vertices erasing segment 1 (vno[0] = 68001) erasing segment 2 (vno[0] = 82907) erasing segment 3 (vno[0] = 86409) erasing segment 4 (vno[0] = 92933) erasing segment 5 (vno[0] = 95578) erasing segment 6 (vno[0] = 104383) erasing segment 7 (vno[0] = 106656) erasing segment 8 (vno[0] = 131101) erasing segment 9 (vno[0] = 132440) erasing segment 10 (vno[0] = 133460) erasing segment 11 (vno[0] = 134545) erasing segment 12 (vno[0] = 135695) erasing segment 13 (vno[0] = 150594) erasing segment 14 (vno[0] = 176592) writing cortex label to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label... writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area vertex spacing 0.88 +- 0.27 (0.01-->8.27) (max @ vno 175712 --> 175715) face area 0.33 +- 0.18 (0.00-->9.56) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 0 with 3 points - only 0.00% unknown deleting segment 1 with 31 points - only 0.00% unknown deleting segment 3 with 13 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 5 with 4 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 6 with 4 points - only 0.00% unknown deleting segment 7 with 23 points - only 0.00% unknown deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 41 points - only 0.00% unknown removing 2 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 12 with 5 points - only 0.00% unknown removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=62.2, 302 (302) missing vertices, mean dist 1.6 [1.1 (%0.0)->2.7 (%100.0))] %16 local maxima, %40 large gradients and %40 min vals, 300 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=28939954.0, rms=28.758 001: dt: 0.0500, sse=26100296.0, rms=27.267 (5.186%) 002: dt: 0.0500, sse=24073462.0, rms=26.150 (4.096%) 003: dt: 0.0500, sse=22518840.0, rms=25.260 (3.404%) 004: dt: 0.0500, sse=21255438.0, rms=24.513 (2.958%) 005: dt: 0.0500, sse=20185418.0, rms=23.861 (2.657%) 006: dt: 0.0500, sse=19252574.0, rms=23.279 (2.442%) 007: dt: 0.0500, sse=18421404.0, rms=22.747 (2.285%) 008: dt: 0.0500, sse=17667624.0, rms=22.253 (2.169%) 009: dt: 0.0500, sse=16976052.0, rms=21.791 (2.078%) 010: dt: 0.0500, sse=16336131.0, rms=21.354 (2.005%) positioning took 0.9 minutes mean border=62.0, 217 (165) missing vertices, mean dist 1.3 [0.7 (%0.1)->2.2 (%99.9))] %17 local maxima, %40 large gradients and %39 min vals, 285 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=17482282.0, rms=22.126 011: dt: 0.0500, sse=16878214.0, rms=21.721 (1.833%) 012: dt: 0.0500, sse=16311120.0, rms=21.333 (1.786%) 013: dt: 0.0500, sse=15776996.0, rms=20.961 (1.743%) 014: dt: 0.0500, sse=15272761.0, rms=20.604 (1.705%) 015: dt: 0.0500, sse=14795598.0, rms=20.260 (1.670%) 016: dt: 0.0500, sse=14343268.0, rms=19.928 (1.637%) 017: dt: 0.0500, sse=13913668.0, rms=19.608 (1.607%) 018: dt: 0.0500, sse=13505470.0, rms=19.299 (1.577%) 019: dt: 0.0500, sse=13117257.0, rms=19.000 (1.549%) 020: dt: 0.0500, sse=12747932.0, rms=18.711 (1.520%) positioning took 0.9 minutes mean border=61.9, 225 (135) missing vertices, mean dist 1.1 [0.1 (%0.7)->1.8 (%99.3))] %18 local maxima, %40 large gradients and %38 min vals, 251 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=12868536.0, rms=18.810 021: dt: 0.0500, sse=12507157.0, rms=18.524 (1.518%) 022: dt: 0.0500, sse=12162349.0, rms=18.248 (1.493%) 023: dt: 0.0500, sse=11831643.0, rms=17.978 (1.476%) 024: dt: 0.0500, sse=11515949.0, rms=17.717 (1.452%) 025: dt: 0.0500, sse=11213896.0, rms=17.464 (1.430%) 026: dt: 0.0500, sse=10924782.0, rms=17.218 (1.409%) 027: dt: 0.0500, sse=10645667.0, rms=16.977 (1.400%) 028: dt: 0.0500, sse=10374099.0, rms=16.739 (1.402%) 029: dt: 0.0500, sse=10108971.0, rms=16.503 (1.408%) 030: dt: 0.0500, sse=9849846.0, rms=16.269 (1.416%) positioning took 0.9 minutes mean border=61.8, 277 (116) missing vertices, mean dist 0.9 [0.1 (%7.7)->1.6 (%92.3))] %18 local maxima, %40 large gradients and %38 min vals, 255 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=9957723.0, rms=16.366 031: dt: 0.5000, sse=8028888.0, rms=14.523 (11.264%) 032: dt: 0.5000, sse=6482262.5, rms=12.849 (11.522%) 033: dt: 0.5000, sse=5193994.0, rms=11.272 (12.279%) 034: dt: 0.5000, sse=4131298.8, rms=9.774 (13.283%) 035: dt: 0.5000, sse=3328560.0, rms=8.473 (13.310%) 036: dt: 0.5000, sse=2733423.2, rms=7.357 (13.180%) 037: dt: 0.5000, sse=2334487.2, rms=6.506 (11.565%) 038: dt: 0.5000, sse=2073018.9, rms=5.875 (9.698%) 039: dt: 0.5000, sse=1923774.8, rms=5.488 (6.589%) 040: dt: 0.5000, sse=1829368.2, rms=5.221 (4.859%) 041: dt: 0.5000, sse=1782077.8, rms=5.087 (2.570%) 042: dt: 0.5000, sse=1749893.4, rms=4.986 (1.979%) rms = 4.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1734034.9, rms=4.941 (0.909%) 044: dt: 0.2500, sse=1552949.2, rms=4.306 (12.856%) 045: dt: 0.2500, sse=1503908.2, rms=4.133 (4.012%) rms = 4.13, time step reduction 2 of 3 to 0.125... 046: dt: 0.1250, sse=1485921.5, rms=4.064 (1.671%) 047: dt: 0.1250, sse=1462145.9, rms=3.970 (2.321%) rms = 3.95, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1457907.4, rms=3.952 (0.454%) positioning took 2.1 minutes mean border=60.6, 3827 (54) missing vertices, mean dist 0.1 [0.2 (%45.5)->0.5 (%54.5))] %29 local maxima, %31 large gradients and %34 min vals, 174 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1797726.9, rms=4.562 049: dt: 0.5000, sse=1757348.6, rms=4.448 (2.495%) 050: dt: 0.5000, sse=1692719.6, rms=4.255 (4.333%) rms = 4.43, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1510433.6, rms=3.512 (17.457%) 052: dt: 0.2500, sse=1463754.6, rms=3.290 (6.332%) rms = 3.28, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1463125.4, rms=3.285 (0.166%) 054: dt: 0.1250, sse=1416906.0, rms=3.055 (6.976%) rms = 3.02, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1410445.1, rms=3.024 (1.028%) positioning took 1.1 minutes mean border=59.8, 4248 (41) missing vertices, mean dist 0.1 [0.1 (%45.9)->0.3 (%54.1))] %39 local maxima, %22 large gradients and %33 min vals, 215 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1477251.1, rms=3.361 rms = 3.80, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1426725.9, rms=3.123 (7.056%) 057: dt: 0.2500, sse=1409325.4, rms=3.044 (2.540%) rms = 3.05, time step reduction 2 of 3 to 0.125... rms = 3.01, time step reduction 3 of 3 to 0.062... 058: dt: 0.1250, sse=1403009.0, rms=3.011 (1.102%) positioning took 0.6 minutes mean border=59.3, 6840 (40) missing vertices, mean dist 0.1 [0.1 (%47.3)->0.3 (%52.7))] %42 local maxima, %18 large gradients and %32 min vals, 218 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=1429170.2, rms=3.138 rms = 3.54, time step reduction 1 of 3 to 0.250... 059: dt: 0.2500, sse=1399239.4, rms=2.988 (4.767%) 060: dt: 0.2500, sse=1383956.5, rms=2.926 (2.069%) rms = 2.93, time step reduction 2 of 3 to 0.125... rms = 2.89, time step reduction 3 of 3 to 0.062... 061: dt: 0.1250, sse=1378340.4, rms=2.895 (1.075%) positioning took 0.6 minutes writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area.pial vertex spacing 0.97 +- 0.41 (0.06-->10.01) (max @ vno 75263 --> 78976) face area 0.37 +- 0.29 (0.00-->17.05) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 177022 vertices processed 25000 of 177022 vertices processed 50000 of 177022 vertices processed 75000 of 177022 vertices processed 100000 of 177022 vertices processed 125000 of 177022 vertices processed 150000 of 177022 vertices processed 175000 of 177022 vertices processed 0 of 177022 vertices processed 25000 of 177022 vertices processed 50000 of 177022 vertices processed 75000 of 177022 vertices processed 100000 of 177022 vertices processed 125000 of 177022 vertices processed 150000 of 177022 vertices processed 175000 of 177022 vertices processed thickness calculation complete, 111:398 truncations. 47387 vertices at 0 distance 136045 vertices at 1 distance 100051 vertices at 2 distance 38198 vertices at 3 distance 12185 vertices at 4 distance 4005 vertices at 5 distance 1489 vertices at 6 distance 548 vertices at 7 distance 205 vertices at 8 distance 79 vertices at 9 distance 45 vertices at 10 distance 31 vertices at 11 distance 21 vertices at 12 distance 19 vertices at 13 distance 9 vertices at 14 distance 7 vertices at 15 distance 7 vertices at 16 distance 12 vertices at 17 distance 10 vertices at 18 distance 6 vertices at 19 distance 11 vertices at 20 distance writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.thickness positioning took 12.9 minutes #-------------------------------------------- #@# Make Pial Surf rh Fri Sep 27 05:12:10 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs BIO-ALS-701-088-BL rh using white.preaparc starting white location... using white.preaparc starting pial locations... using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/filled.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/brain.finalsurfs.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/../mri/aseg.presurf.mgz... reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... 31503 bright wm thresholded. 4021 bright non-wm voxels segmented. reading original surface position from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.orig... computing class statistics... border white: 349585 voxels (2.08%) border gray 375151 voxels (2.24%) WM (98.0): 98.8 +- 7.1 [70.0 --> 110.0] GM (78.0) : 75.9 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 66.9 (was 70) setting MAX_BORDER_WHITE to 109.1 (was 105) setting MIN_BORDER_WHITE to 78.0 (was 85) setting MAX_CSF to 55.8 (was 40) setting MAX_GRAY to 94.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 66.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 44.7 (was 40) using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102+-6.1, GM=78+-7.8 mean inside = 95.1, mean outside = 80.2 smoothing surface for 5 iterations... reading initial white vertex positions from white.preaparc... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.88 +- 0.26 (0.01-->8.65) (max @ vno 175139 --> 175243) face area 0.32 +- 0.17 (0.00-->6.84) mean absolute distance = 0.69 +- 0.96 4066 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 2 with 17 points - only 0.00% unknown deleting segment 3 with 107 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 3 points - only 0.00% unknown deleting segment 5 with 80 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 7 with 1 points - only 0.00% unknown mean border=86.7, 154 (154) missing vertices, mean dist 0.3 [1.1 (%15.9)->0.6 (%84.1))] %53 local maxima, %43 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.26 (0.08-->8.81) (max @ vno 175243 --> 175139) face area 0.32 +- 0.16 (0.00-->6.66) mean absolute distance = 0.42 +- 0.71 6000 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2114772.8, rms=6.125 001: dt: 0.5000, sse=1310801.5, rms=3.734 (39.031%) 002: dt: 0.5000, sse=1074080.5, rms=2.670 (28.507%) 003: dt: 0.5000, sse=1024930.1, rms=2.412 (9.655%) 004: dt: 0.5000, sse=997791.1, rms=2.275 (5.694%) rms = 2.34, time step reduction 1 of 3 to 0.250... 005: dt: 0.2500, sse=934102.9, rms=1.777 (21.871%) 006: dt: 0.2500, sse=909393.0, rms=1.528 (13.991%) 007: dt: 0.2500, sse=905374.6, rms=1.466 (4.071%) rms = 1.44, time step reduction 2 of 3 to 0.125... 008: dt: 0.2500, sse=903348.9, rms=1.443 (1.569%) rms = 1.42, time step reduction 3 of 3 to 0.062... 009: dt: 0.1250, sse=906481.9, rms=1.419 (1.648%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 0.00% unknown deleting segment 1 with 21 points - only 0.00% unknown deleting segment 2 with 67 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 64 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown mean border=88.9, 121 (47) missing vertices, mean dist -0.3 [0.5 (%64.6)->0.2 (%35.4))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.26 (0.08-->8.87) (max @ vno 175243 --> 175139) face area 0.34 +- 0.17 (0.00-->7.67) mean absolute distance = 0.34 +- 0.50 7129 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1287915.2, rms=3.465 010: dt: 0.5000, sse=1047466.2, rms=2.223 (35.846%) 011: dt: 0.5000, sse=1002276.0, rms=1.947 (12.409%) rms = 1.98, time step reduction 1 of 3 to 0.250... 012: dt: 0.2500, sse=957556.2, rms=1.564 (19.662%) 013: dt: 0.2500, sse=942370.2, rms=1.338 (14.439%) 014: dt: 0.2500, sse=932527.1, rms=1.281 (4.292%) rms = 1.25, time step reduction 2 of 3 to 0.125... 015: dt: 0.2500, sse=930022.8, rms=1.253 (2.196%) rms = 1.23, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=929262.8, rms=1.233 (1.601%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 13 points - only 0.00% unknown deleting segment 1 with 23 points - only 0.00% unknown deleting segment 2 with 88 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 73 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 5 with 2 points - only 0.00% unknown mean border=90.7, 130 (32) missing vertices, mean dist -0.2 [0.4 (%66.2)->0.2 (%33.8))] %78 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.05-->8.94) (max @ vno 175243 --> 175139) face area 0.33 +- 0.17 (0.00-->8.04) mean absolute distance = 0.28 +- 0.41 5658 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=1110453.8, rms=2.742 017: dt: 0.5000, sse=980476.0, rms=1.832 (33.160%) rms = 1.79, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=967505.4, rms=1.792 (2.183%) 019: dt: 0.2500, sse=939561.7, rms=1.270 (29.162%) 020: dt: 0.2500, sse=906992.6, rms=1.181 (6.962%) rms = 1.18, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=904073.2, rms=1.179 (0.179%) rms = 1.15, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=900668.6, rms=1.152 (2.287%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 24 points - only 0.00% unknown deleting segment 2 with 94 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown deleting segment 4 with 75 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 8 points - only 0.00% unknown mean border=91.5, 162 (22) missing vertices, mean dist -0.1 [0.3 (%56.0)->0.2 (%44.0))] %83 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=929025.1, rms=1.596 023: dt: 0.5000, sse=913139.9, rms=1.225 (23.201%) rms = 1.57, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=875362.3, rms=0.994 (18.919%) rms = 0.98, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=894520.5, rms=0.979 (1.463%) rms = 0.94, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=870762.9, rms=0.935 (4.465%) positioning took 0.4 minutes generating cortex label... 9 non-cortical segments detected only using segment with 8105 vertices erasing segment 1 (vno[0] = 89069) erasing segment 2 (vno[0] = 93812) erasing segment 3 (vno[0] = 104718) erasing segment 4 (vno[0] = 123177) erasing segment 5 (vno[0] = 129025) erasing segment 6 (vno[0] = 132395) erasing segment 7 (vno[0] = 140402) erasing segment 8 (vno[0] = 158201) writing cortex label to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label... writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area vertex spacing 0.88 +- 0.27 (0.04-->9.02) (max @ vno 175139 --> 175243) face area 0.33 +- 0.17 (0.00-->7.71) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 41 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 1 with 4 points - only 0.00% unknown deleting segment 2 with 21 points - only 0.00% unknown deleting segment 7 with 18 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown deleting segment 9 with 72 points - only 0.00% unknown deleting segment 10 with 9 points - only 0.00% unknown deleting segment 11 with 60 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from white.preaparc... mean border=64.6, 231 (231) missing vertices, mean dist 1.6 [0.5 (%0.0)->2.6 (%100.0))] %18 local maxima, %43 large gradients and %35 min vals, 405 gradients ignored perforing initial smooth deformation to move away from white surface tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=26933532.0, rms=27.707 001: dt: 0.0500, sse=24241956.0, rms=26.240 (5.295%) 002: dt: 0.0500, sse=22322378.0, rms=25.141 (4.187%) 003: dt: 0.0500, sse=20849236.0, rms=24.264 (3.488%) 004: dt: 0.0500, sse=19651268.0, rms=23.527 (3.039%) 005: dt: 0.0500, sse=18637466.0, rms=22.884 (2.732%) 006: dt: 0.0500, sse=17755200.0, rms=22.310 (2.510%) 007: dt: 0.0500, sse=16969832.0, rms=21.786 (2.349%) 008: dt: 0.0500, sse=16258618.0, rms=21.300 (2.230%) 009: dt: 0.0500, sse=15606934.0, rms=20.845 (2.137%) 010: dt: 0.0500, sse=15003467.0, rms=20.414 (2.065%) positioning took 0.9 minutes mean border=64.4, 168 (100) missing vertices, mean dist 1.3 [0.3 (%0.1)->2.1 (%99.9))] %19 local maxima, %43 large gradients and %34 min vals, 377 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=16177898.0, rms=21.240 011: dt: 0.0500, sse=15609200.0, rms=20.843 (1.871%) 012: dt: 0.0500, sse=15076002.0, rms=20.463 (1.822%) 013: dt: 0.0500, sse=14574703.0, rms=20.099 (1.777%) 014: dt: 0.0500, sse=14101790.0, rms=19.750 (1.737%) 015: dt: 0.0500, sse=13654872.0, rms=19.414 (1.701%) 016: dt: 0.0500, sse=13231869.0, rms=19.091 (1.666%) 017: dt: 0.0500, sse=12830902.0, rms=18.779 (1.633%) 018: dt: 0.0500, sse=12451275.0, rms=18.479 (1.598%) 019: dt: 0.0500, sse=12090509.0, rms=18.189 (1.568%) 020: dt: 0.0500, sse=11747277.0, rms=17.909 (1.540%) positioning took 0.8 minutes mean border=64.2, 178 (77) missing vertices, mean dist 1.1 [0.1 (%0.9)->1.7 (%99.1))] %19 local maxima, %43 large gradients and %33 min vals, 379 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.05 000: dt: 0.0000, sse=11887294.0, rms=18.028 021: dt: 0.0500, sse=11549753.0, rms=17.750 (1.542%) 022: dt: 0.0500, sse=11228298.0, rms=17.481 (1.515%) 023: dt: 0.0500, sse=10919921.0, rms=17.219 (1.498%) 024: dt: 0.0500, sse=10625669.0, rms=16.966 (1.474%) 025: dt: 0.0500, sse=10344630.0, rms=16.720 (1.450%) 026: dt: 0.0500, sse=10075212.0, rms=16.480 (1.432%) 027: dt: 0.0500, sse=9815574.0, rms=16.246 (1.420%) 028: dt: 0.0500, sse=9562727.0, rms=16.015 (1.424%) 029: dt: 0.0500, sse=9315908.0, rms=15.786 (1.431%) 030: dt: 0.0500, sse=9074573.0, rms=15.558 (1.440%) positioning took 0.9 minutes mean border=64.1, 186 (55) missing vertices, mean dist 0.9 [0.1 (%9.2)->1.5 (%90.8))] %20 local maxima, %43 large gradients and %33 min vals, 357 gradients ignored tol=1.0e-04, sigma=2.0, host=aura., nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=9198402.0, rms=15.673 031: dt: 0.5000, sse=7378414.5, rms=13.856 (11.592%) 032: dt: 0.5000, sse=5963558.5, rms=12.253 (11.573%) 033: dt: 0.5000, sse=4819356.5, rms=10.787 (11.965%) 034: dt: 0.5000, sse=3903119.5, rms=9.443 (12.454%) 035: dt: 0.5000, sse=3227783.5, rms=8.318 (11.921%) 036: dt: 0.5000, sse=2717327.5, rms=7.347 (11.673%) 037: dt: 0.5000, sse=2357115.8, rms=6.581 (10.420%) 038: dt: 0.5000, sse=2101666.2, rms=5.971 (9.271%) 039: dt: 0.5000, sse=1936721.0, rms=5.548 (7.079%) 040: dt: 0.5000, sse=1819993.2, rms=5.220 (5.922%) 041: dt: 0.5000, sse=1757788.1, rms=5.042 (3.408%) 042: dt: 0.5000, sse=1714224.0, rms=4.906 (2.698%) rms = 4.86, time step reduction 1 of 3 to 0.250... 043: dt: 0.5000, sse=1698828.4, rms=4.862 (0.891%) 044: dt: 0.2500, sse=1515310.1, rms=4.208 (13.456%) 045: dt: 0.2500, sse=1464773.0, rms=4.026 (4.326%) rms = 4.02, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=1463730.0, rms=4.017 (0.222%) 047: dt: 0.1250, sse=1423646.0, rms=3.859 (3.921%) rms = 3.84, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=1418329.0, rms=3.838 (0.553%) positioning took 2.0 minutes mean border=62.6, 3486 (16) missing vertices, mean dist 0.1 [0.2 (%43.6)->0.5 (%56.4))] %33 local maxima, %32 large gradients and %30 min vals, 159 gradients ignored tol=1.0e-04, sigma=1.0, host=aura., nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1837847.9, rms=4.696 049: dt: 0.5000, sse=1737352.9, rms=4.385 (6.619%) 050: dt: 0.5000, sse=1670950.0, rms=4.180 (4.695%) rms = 4.32, time step reduction 1 of 3 to 0.250... 051: dt: 0.2500, sse=1482168.1, rms=3.394 (18.784%) 052: dt: 0.2500, sse=1431090.9, rms=3.143 (7.397%) rms = 3.12, time step reduction 2 of 3 to 0.125... 053: dt: 0.2500, sse=1427225.6, rms=3.123 (0.638%) 054: dt: 0.1250, sse=1380862.1, rms=2.882 (7.734%) rms = 2.84, time step reduction 3 of 3 to 0.062... 055: dt: 0.1250, sse=1372667.6, rms=2.840 (1.460%) positioning took 1.0 minutes mean border=61.7, 3734 (12) missing vertices, mean dist 0.1 [0.2 (%43.2)->0.3 (%56.8))] %43 local maxima, %22 large gradients and %29 min vals, 179 gradients ignored tol=1.0e-04, sigma=0.5, host=aura., nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1476486.4, rms=3.355 rms = 3.74, time step reduction 1 of 3 to 0.250... 056: dt: 0.2500, sse=1409715.6, rms=3.038 (9.432%) 057: dt: 0.2500, sse=1380185.6, rms=2.891 (4.861%) rms = 2.89, time step reduction 2 of 3 to 0.125... 058: dt: 0.2500, sse=1378204.6, rms=2.888 (0.100%) 059: dt: 0.1250, sse=1356105.4, rms=2.765 (4.263%) rms = 2.74, time step reduction 3 of 3 to 0.062... 060: dt: 0.1250, sse=1350193.6, rms=2.735 (1.062%) positioning took 0.8 minutes mean border=61.1, 5837 (10) missing vertices, mean dist 0.1 [0.2 (%45.6)->0.3 (%54.4))] %47 local maxima, %18 large gradients and %28 min vals, 185 gradients ignored tol=1.0e-04, sigma=0.2, host=aura., nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=1378044.1, rms=2.884 rms = 3.31, time step reduction 1 of 3 to 0.250... 061: dt: 0.2500, sse=1350314.0, rms=2.734 (5.227%) 062: dt: 0.2500, sse=1338406.2, rms=2.680 (1.970%) rms = 2.69, time step reduction 2 of 3 to 0.125... rms = 2.65, time step reduction 3 of 3 to 0.062... 063: dt: 0.1250, sse=1333343.9, rms=2.649 (1.148%) positioning took 0.6 minutes writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area.pial vertex spacing 0.97 +- 0.41 (0.06-->8.93) (max @ vno 175243 --> 175139) face area 0.38 +- 0.29 (0.00-->8.55) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 177054 vertices processed 25000 of 177054 vertices processed 50000 of 177054 vertices processed 75000 of 177054 vertices processed 100000 of 177054 vertices processed 125000 of 177054 vertices processed 150000 of 177054 vertices processed 175000 of 177054 vertices processed 0 of 177054 vertices processed 25000 of 177054 vertices processed 50000 of 177054 vertices processed 75000 of 177054 vertices processed 100000 of 177054 vertices processed 125000 of 177054 vertices processed 150000 of 177054 vertices processed 175000 of 177054 vertices processed thickness calculation complete, 225:586 truncations. 47824 vertices at 0 distance 134598 vertices at 1 distance 100748 vertices at 2 distance 38941 vertices at 3 distance 12432 vertices at 4 distance 3823 vertices at 5 distance 1224 vertices at 6 distance 449 vertices at 7 distance 169 vertices at 8 distance 61 vertices at 9 distance 26 vertices at 10 distance 27 vertices at 11 distance 24 vertices at 12 distance 23 vertices at 13 distance 15 vertices at 14 distance 15 vertices at 15 distance 16 vertices at 16 distance 9 vertices at 17 distance 7 vertices at 18 distance 3 vertices at 19 distance 10 vertices at 20 distance writing curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.thickness positioning took 12.8 minutes #-------------------------------------------- #@# Surf Volume lh Fri Sep 27 05:24:56 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume BIO-ALS-701-088-BL lh /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.volume masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label Total face volume 287758 Total vertex volume 285088 (mask=0) #@# BIO-ALS-701-088-BL lh 285088 vertexvol Done #-------------------------------------------- #@# Surf Volume rh Fri Sep 27 05:24:59 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume BIO-ALS-701-088-BL rh /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.volume masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label Total face volume 290552 Total vertex volume 287212 (mask=0) #@# BIO-ALS-701-088-BL rh 287212 vertexvol Done #-------------------------------------------- #@# Cortical ribbon mask Fri Sep 27 05:25:03 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL SUBJECTS_DIR is /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 133 writing volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/ribbon.mgz mris_volmask took 10.59 minutes writing ribbon files #----------------------------------------- #@# Parcellation Stats lh Fri Sep 27 05:35:38 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 287758 Total vertex volume 285088 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1946 1365 3208 2.565 0.468 0.112 0.022 14 1.5 bankssts 1194 798 2200 2.461 0.763 0.143 0.024 19 1.1 caudalanteriorcingulate 4423 2841 7445 2.539 0.526 0.117 0.031 54 6.0 caudalmiddlefrontal 3988 2572 4405 1.711 0.428 0.145 0.040 51 6.6 cuneus 397 277 1491 3.996 0.604 0.120 0.029 3 0.4 entorhinal 4617 3092 8637 2.539 0.592 0.120 0.028 49 4.9 fusiform 8530 5746 13864 2.296 0.484 0.130 0.031 97 10.9 inferiorparietal 6903 4627 13911 2.688 0.714 0.142 0.043 114 12.6 inferiortemporal 1768 1139 2873 2.383 0.897 0.131 0.038 26 2.4 isthmuscingulate 10394 6800 15901 2.187 0.547 0.138 0.035 145 16.0 lateraloccipital 5096 3333 9229 2.595 0.649 0.136 0.039 70 9.2 lateralorbitofrontal 5603 3860 8120 1.987 0.535 0.145 0.039 80 8.6 lingual 3290 2172 5418 2.358 0.609 0.127 0.035 48 4.6 medialorbitofrontal 7972 5065 16792 2.790 0.663 0.125 0.036 119 12.9 middletemporal 1312 905 2605 2.512 0.738 0.100 0.036 18 1.9 parahippocampal 2787 1705 4194 2.319 0.529 0.119 0.032 31 3.8 paracentral 2584 1685 5062 2.756 0.482 0.110 0.029 25 2.7 parsopercularis 1371 888 2902 2.708 0.470 0.138 0.034 19 1.7 parsorbitalis 2254 1461 4134 2.519 0.536 0.118 0.025 22 2.2 parstriangularis 2758 2158 2861 1.512 0.465 0.175 0.050 44 6.9 pericalcarine 7899 4823 10649 2.062 0.606 0.116 0.033 85 10.2 postcentral 2384 1504 4002 2.382 0.869 0.140 0.035 39 3.0 posteriorcingulate 9539 5656 14288 2.466 0.642 0.116 0.034 159 14.2 precentral 7269 4905 11697 2.315 0.566 0.134 0.036 84 10.3 precuneus 1386 940 3097 2.725 0.710 0.142 0.035 26 2.1 rostralanteriorcingulate 13238 8621 21320 2.228 0.526 0.128 0.031 162 16.1 rostralmiddlefrontal 14022 9359 27934 2.627 0.596 0.127 0.031 162 17.9 superiorfrontal 10648 6855 14819 2.044 0.498 0.121 0.029 112 12.4 superiorparietal 7899 4959 15553 2.813 0.661 0.105 0.027 75 9.2 superiortemporal 8012 5017 12848 2.472 0.571 0.130 0.039 110 12.3 supramarginal 441 289 1012 2.556 0.519 0.160 0.044 8 0.8 frontalpole 712 513 2573 3.489 0.729 0.144 0.037 9 1.2 temporalpole 1091 658 1389 2.002 0.534 0.134 0.049 19 2.5 transversetemporal 4975 3211 8617 2.672 0.913 0.117 0.039 74 7.2 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 BIO-ALS-701-088-BL lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 287758 Total vertex volume 285088 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1946 1156 3208 2.565 0.468 0.117 0.031 28 2.7 bankssts 1194 974 2200 2.461 0.763 0.153 0.038 55 1.8 caudalanteriorcingulate 4423 2976 7445 2.539 0.526 0.107 0.023 45 4.4 caudalmiddlefrontal 3988 2713 4405 1.711 0.428 0.126 0.034 59 6.4 cuneus 397 453 1491 3.996 0.604 0.168 0.041 12 0.7 entorhinal 4617 3653 8637 2.539 0.592 0.140 0.033 71 7.1 fusiform 8530 6494 13864 2.296 0.484 0.137 0.032 123 12.4 inferiorparietal 6903 5586 13911 2.688 0.714 0.149 0.039 112 12.4 inferiortemporal 1768 1263 2873 2.383 0.897 0.131 0.037 35 2.8 isthmuscingulate 10394 7923 15901 2.187 0.547 0.128 0.029 165 13.8 lateraloccipital 5096 3703 9229 2.595 0.649 0.133 0.036 82 8.6 lateralorbitofrontal 5603 4471 8120 1.987 0.535 0.142 0.036 107 9.1 lingual 3290 2513 5418 2.358 0.609 0.137 0.034 44 4.9 medialorbitofrontal 7972 6541 16792 2.790 0.663 0.128 0.029 99 10.4 middletemporal 1312 1192 2605 2.512 0.738 0.131 0.039 12 2.8 parahippocampal 2787 1942 4194 2.319 0.529 0.105 0.036 59 2.8 paracentral 2584 1982 5062 2.756 0.482 0.123 0.029 31 3.4 parsopercularis 1371 1223 2902 2.708 0.470 0.154 0.033 21 2.0 parsorbitalis 2254 1795 4134 2.519 0.536 0.139 0.028 33 2.9 parstriangularis 2758 1851 2861 1.512 0.465 0.124 0.035 43 3.9 pericalcarine 7899 5587 10649 2.062 0.606 0.108 0.022 66 7.3 postcentral 2384 1717 4002 2.382 0.869 0.144 0.050 173 6.8 posteriorcingulate 9539 6030 14288 2.466 0.642 0.094 0.021 91 8.6 precentral 7269 5253 11697 2.315 0.566 0.134 0.033 122 10.7 precuneus 1386 1332 3097 2.725 0.710 0.166 0.040 18 2.3 rostralanteriorcingulate 13238 10175 21320 2.228 0.526 0.135 0.029 150 16.5 rostralmiddlefrontal 14022 11353 27934 2.627 0.596 0.134 0.029 159 17.7 superiorfrontal 10648 7630 14819 2.044 0.498 0.118 0.025 117 11.5 superiorparietal 7899 5942 15553 2.813 0.661 0.119 0.027 98 10.1 superiortemporal 8012 5283 12848 2.472 0.571 0.119 0.033 121 11.3 supramarginal 441 504 1012 2.556 0.519 0.188 0.037 4 0.7 frontalpole 712 930 2573 3.489 0.729 0.188 0.036 7 1.2 temporalpole 1091 800 1389 2.002 0.534 0.129 0.042 11 2.2 transversetemporal 4975 3037 8617 2.672 0.913 0.132 0.078 256 22.7 insula #----------------------------------------- #@# Parcellation Stats rh Fri Sep 27 05:36:46 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 290552 Total vertex volume 287212 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1568 1123 2751 2.619 0.441 0.116 0.023 13 1.4 bankssts 780 537 1139 2.238 0.410 0.135 0.019 13 0.6 caudalanteriorcingulate 3908 2560 7557 2.606 0.536 0.115 0.028 41 4.4 caudalmiddlefrontal 3742 2313 4205 1.783 0.416 0.136 0.036 46 6.0 cuneus 462 301 1763 3.811 0.797 0.111 0.024 3 0.5 entorhinal 6581 4333 12264 2.558 0.609 0.131 0.038 92 10.1 fusiform 10547 6855 18171 2.390 0.550 0.126 0.029 121 12.5 inferiorparietal 5458 3642 10594 2.699 0.642 0.130 0.034 75 7.5 inferiortemporal 2035 1323 3370 2.318 0.730 0.137 0.043 32 3.3 isthmuscingulate 11236 7383 17042 2.199 0.550 0.137 0.036 143 16.7 lateraloccipital 4706 3009 8368 2.575 0.610 0.135 0.041 73 8.6 lateralorbitofrontal 6556 4486 9509 2.013 0.499 0.151 0.044 98 12.4 lingual 3805 2505 6595 2.299 0.693 0.124 0.036 60 5.7 medialorbitofrontal 6878 4482 15072 2.840 0.607 0.119 0.028 85 7.2 middletemporal 1222 818 2200 2.414 0.675 0.100 0.031 10 1.7 parahippocampal 3095 1780 4229 2.331 0.541 0.125 0.044 39 5.8 paracentral 2114 1354 4212 2.792 0.460 0.106 0.020 16 1.8 parsopercularis 1573 919 2845 2.506 0.482 0.126 0.039 25 2.7 parsorbitalis 2928 1900 5251 2.457 0.486 0.133 0.038 40 4.4 parstriangularis 3155 2395 3382 1.551 0.419 0.161 0.043 51 5.7 pericalcarine 7805 4692 10537 2.096 0.639 0.111 0.031 95 9.6 postcentral 2185 1455 3644 2.351 0.695 0.147 0.042 38 3.3 posteriorcingulate 9117 5509 13826 2.440 0.612 0.113 0.031 90 12.1 precentral 8554 5491 12820 2.259 0.544 0.130 0.038 114 14.0 precuneus 761 492 1161 2.581 0.753 0.121 0.022 9 0.6 rostralanteriorcingulate 12534 8248 22093 2.376 0.547 0.129 0.034 171 17.9 rostralmiddlefrontal 13300 8923 28405 2.666 0.611 0.126 0.032 164 17.5 superiorfrontal 9979 6337 14038 2.084 0.482 0.115 0.028 101 11.1 superiorparietal 8048 5038 15488 2.807 0.711 0.110 0.030 86 10.0 superiortemporal 6933 4323 10904 2.410 0.527 0.112 0.032 83 9.1 supramarginal 586 351 1240 2.497 0.587 0.180 0.075 18 1.9 frontalpole 718 483 2676 3.952 0.587 0.124 0.034 8 1.0 temporalpole 666 405 1006 2.131 0.663 0.129 0.043 15 1.2 transversetemporal 4918 3249 8814 2.809 0.772 0.127 0.045 69 9.4 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 BIO-ALS-701-088-BL rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 290552 Total vertex volume 287212 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1568 966 2751 2.619 0.441 0.121 0.034 22 2.3 bankssts 780 551 1139 2.238 0.410 0.146 0.037 20 1.1 caudalanteriorcingulate 3908 3052 7557 2.606 0.536 0.115 0.024 47 4.0 caudalmiddlefrontal 3742 2560 4205 1.783 0.416 0.113 0.025 45 4.0 cuneus 462 536 1763 3.811 0.797 0.165 0.036 6 0.7 entorhinal 6581 5086 12264 2.558 0.609 0.138 0.042 268 12.9 fusiform 10547 8224 18171 2.390 0.550 0.132 0.029 125 13.3 inferiorparietal 5458 4123 10594 2.699 0.642 0.131 0.031 92 7.7 inferiortemporal 2035 1511 3370 2.318 0.730 0.125 0.032 34 2.5 isthmuscingulate 11236 8288 17042 2.199 0.550 0.127 0.031 173 15.9 lateraloccipital 4706 3560 8368 2.575 0.610 0.148 0.038 72 8.1 lateralorbitofrontal 6556 5129 9509 2.013 0.499 0.140 0.037 105 11.2 lingual 3805 3254 6595 2.299 0.693 0.157 0.038 51 6.6 medialorbitofrontal 6878 5974 15072 2.840 0.607 0.135 0.030 77 9.3 middletemporal 1222 1003 2200 2.414 0.675 0.122 0.026 12 1.5 parahippocampal 3095 1863 4229 2.331 0.541 0.105 0.038 53 6.4 paracentral 2114 1636 4212 2.792 0.460 0.125 0.027 25 2.6 parsopercularis 1573 1322 2845 2.506 0.482 0.133 0.026 19 1.8 parsorbitalis 2928 2371 5251 2.457 0.486 0.156 0.040 47 5.7 parstriangularis 3155 2157 3382 1.551 0.419 0.125 0.035 39 4.2 pericalcarine 7805 5462 10537 2.096 0.639 0.109 0.022 63 7.4 postcentral 2185 1610 3644 2.351 0.695 0.142 0.040 54 3.6 posteriorcingulate 9117 5862 13826 2.440 0.612 0.097 0.021 92 8.7 precentral 8554 5704 12820 2.259 0.544 0.119 0.031 117 11.3 precuneus 761 538 1161 2.581 0.753 0.147 0.036 18 1.3 rostralanteriorcingulate 12534 9987 22093 2.376 0.547 0.142 0.030 156 16.8 rostralmiddlefrontal 13300 11544 28405 2.666 0.611 0.145 0.032 155 18.6 superiorfrontal 9979 7097 14038 2.084 0.482 0.115 0.024 95 10.1 superiorparietal 8048 5875 15488 2.807 0.711 0.120 0.027 135 10.0 superiortemporal 6933 4561 10904 2.410 0.527 0.110 0.025 71 7.5 supramarginal 586 626 1240 2.497 0.587 0.209 0.042 10 1.3 frontalpole 718 857 2676 3.952 0.587 0.158 0.028 5 0.9 temporalpole 666 526 1006 2.131 0.663 0.123 0.031 6 0.9 transversetemporal 4918 3027 8814 2.809 0.772 0.134 0.045 116 8.4 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Sep 27 05:37:55 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL lh ../surf/lh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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... 119 labels changed using aseg relabeling using gibbs priors... 000: 11429 changed, 177022 examined... 001: 2679 changed, 44316 examined... 002: 808 changed, 14055 examined... 003: 340 changed, 4597 examined... 004: 149 changed, 1889 examined... 005: 73 changed, 857 examined... 006: 49 changed, 444 examined... 007: 35 changed, 255 examined... 008: 16 changed, 170 examined... 009: 10 changed, 98 examined... 010: 10 changed, 59 examined... 011: 7 changed, 59 examined... 012: 4 changed, 45 examined... 013: 3 changed, 32 examined... 014: 1 changed, 21 examined... 015: 1 changed, 7 examined... 016: 0 changed, 5 examined... 13 labels changed using aseg 000: 359 total segments, 272 labels (3880 vertices) changed 001: 116 total segments, 32 labels (123 vertices) changed 002: 86 total segments, 2 labels (17 vertices) changed 003: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 45 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1669 vertices marked for relabeling... 1669 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 18 seconds. #----------------------------------------- #@# Cortical Parc 2 rh Fri Sep 27 05:38:14 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL rh ../surf/rh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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: 11485 changed, 177054 examined... 001: 2816 changed, 44990 examined... 002: 830 changed, 14510 examined... 003: 334 changed, 4568 examined... 004: 161 changed, 1938 examined... 005: 80 changed, 898 examined... 006: 41 changed, 459 examined... 007: 23 changed, 225 examined... 008: 17 changed, 127 examined... 009: 5 changed, 98 examined... 010: 1 changed, 28 examined... 011: 1 changed, 6 examined... 012: 1 changed, 8 examined... 013: 0 changed, 7 examined... 60 labels changed using aseg 000: 306 total segments, 217 labels (3868 vertices) changed 001: 108 total segments, 21 labels (663 vertices) changed 002: 87 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1358 vertices marked for relabeling... 1358 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 17 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Sep 27 05:38:31 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 287758 Total vertex volume 285088 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1614 1042 2488 2.207 0.539 0.128 0.031 18 2.1 G&S_frontomargin 1881 1250 3414 2.434 0.461 0.143 0.040 28 3.1 G&S_occipital_inf 1982 1184 2752 2.118 0.464 0.125 0.037 25 3.0 G&S_paracentral 2094 1263 3607 2.553 0.555 0.121 0.040 28 3.7 G&S_subcentral 1107 693 2007 2.286 0.448 0.149 0.042 21 1.8 G&S_transv_frontopol 2770 1896 5597 2.752 0.549 0.129 0.029 34 3.3 G&S_cingul-Ant 1704 1162 3137 2.662 0.506 0.121 0.023 17 1.6 G&S_cingul-Mid-Ant 1788 1217 3193 2.576 0.543 0.131 0.030 20 2.0 G&S_cingul-Mid-Post 778 493 1764 2.786 0.702 0.140 0.047 12 1.3 G_cingul-Post-dorsal 419 249 919 2.939 0.571 0.115 0.042 6 0.6 G_cingul-Post-ventral 3360 2213 4005 1.685 0.453 0.150 0.041 43 5.9 G_cuneus 1683 1003 3969 2.907 0.516 0.123 0.043 28 3.0 G_front_inf-Opercular 564 351 1330 2.754 0.309 0.154 0.045 12 0.9 G_front_inf-Orbital 1271 783 2699 2.638 0.535 0.125 0.032 16 1.5 G_front_inf-Triangul 7372 4561 14242 2.506 0.534 0.134 0.038 123 11.4 G_front_middle 9686 6303 21402 2.743 0.607 0.135 0.037 134 14.8 G_front_sup 930 580 1669 2.762 0.832 0.127 0.053 14 1.8 G_Ins_lg&S_cent_ins 876 560 2706 3.456 0.626 0.129 0.036 14 1.1 G_insular_short 3616 2308 6735 2.379 0.513 0.134 0.030 51 4.6 G_occipital_middle 2419 1405 2899 1.917 0.494 0.128 0.038 30 4.2 G_occipital_sup 1728 1126 3725 2.542 0.496 0.120 0.033 23 2.1 G_oc-temp_lat-fusifor 4069 2815 6314 1.964 0.539 0.153 0.044 65 6.9 G_oc-temp_med-Lingual 1360 896 3369 2.928 0.893 0.118 0.045 22 2.5 G_oc-temp_med-Parahip 3207 2009 6704 2.583 0.697 0.134 0.041 47 5.3 G_orbital 3694 2349 6683 2.347 0.541 0.143 0.038 58 5.6 G_pariet_inf-Angular 4011 2334 7363 2.629 0.623 0.133 0.049 69 8.0 G_pariet_inf-Supramar 4472 2746 7121 2.183 0.534 0.126 0.033 56 5.7 G_parietal_sup 3391 1897 4662 2.116 0.599 0.125 0.038 42 5.0 G_postcentral 3829 1875 5688 2.563 0.741 0.111 0.041 105 6.7 G_precentral 3431 2319 6912 2.416 0.582 0.144 0.041 52 5.5 G_precuneus 1157 735 2057 2.164 0.638 0.150 0.053 25 2.5 G_rectus 1253 706 1437 1.960 1.074 0.097 0.044 19 1.8 G_subcallosal 905 535 1269 2.083 0.513 0.122 0.045 14 1.9 G_temp_sup-G_T_transv 2823 1641 6599 2.939 0.639 0.123 0.036 39 4.5 G_temp_sup-Lateral 1061 706 2872 3.568 0.531 0.089 0.022 10 0.7 G_temp_sup-Plan_polar 932 625 1786 2.552 0.445 0.087 0.020 6 0.6 G_temp_sup-Plan_tempo 3962 2612 8878 2.667 0.680 0.152 0.048 82 8.0 G_temporal_inf 4782 2828 11145 2.891 0.714 0.131 0.044 90 9.5 G_temporal_middle 282 191 376 2.346 0.443 0.105 0.014 2 0.2 Lat_Fis-ant-Horizont 341 242 496 2.506 0.392 0.104 0.023 2 0.2 Lat_Fis-ant-Vertical 1476 999 1819 2.275 0.552 0.138 0.038 17 2.6 Lat_Fis-post 3042 2016 4316 2.009 0.573 0.146 0.043 49 5.9 Pole_occipital 1628 1137 5515 3.466 0.759 0.158 0.047 29 3.5 Pole_temporal 3052 2317 3396 1.772 0.664 0.170 0.048 47 7.1 S_calcarine 3076 2227 3528 1.822 0.594 0.115 0.024 22 3.2 S_central 1136 785 1520 2.199 0.515 0.113 0.024 9 1.0 S_cingul-Marginalis 670 462 1114 2.855 0.528 0.114 0.021 5 0.6 S_circular_insula_ant 1793 1235 2873 2.804 0.694 0.102 0.024 18 2.0 S_circular_insula_inf 2239 1533 3349 2.719 0.445 0.102 0.020 13 1.9 S_circular_insula_sup 956 627 1579 2.774 0.598 0.119 0.026 9 0.9 S_collat_transv_ant 570 399 643 1.917 0.387 0.125 0.026 4 0.7 S_collat_transv_post 3304 2218 4341 2.119 0.427 0.112 0.023 26 3.1 S_front_inf 2546 1736 3242 1.942 0.447 0.117 0.023 21 2.3 S_front_middle 3470 2357 5579 2.344 0.509 0.110 0.023 26 3.5 S_front_sup 391 265 579 2.721 0.481 0.131 0.032 3 0.5 S_interm_prim-Jensen 3871 2663 4865 2.035 0.417 0.116 0.023 31 3.6 S_intrapariet&P_trans 1249 865 1521 2.126 0.409 0.128 0.029 10 1.4 S_oc_middle&Lunatus 1366 1021 1779 2.124 0.516 0.130 0.027 12 1.5 S_oc_sup&transversal 1054 728 1485 2.091 0.517 0.114 0.019 9 0.9 S_occipital_ant 1176 810 1589 2.291 0.580 0.105 0.024 10 1.1 S_oc-temp_lat 2272 1592 3023 2.188 0.488 0.107 0.019 17 1.6 S_oc-temp_med&Lingual 583 413 826 2.155 0.543 0.136 0.027 5 0.7 S_orbital_lateral 803 592 1012 2.226 0.605 0.120 0.020 7 0.6 S_orbital_med-olfact 1973 1329 3376 2.601 0.587 0.132 0.040 25 4.0 S_orbital-H_Shaped 3747 2466 4508 2.101 0.542 0.124 0.031 35 4.7 S_parieto_occipital 1573 952 1031 1.418 0.549 0.142 0.028 35 1.6 S_pericallosal 3872 2543 4689 2.021 0.423 0.119 0.027 39 3.9 S_postcentral 2208 1502 3303 2.531 0.424 0.116 0.025 18 2.2 S_precentral-inf-part 1870 1270 2443 2.298 0.460 0.115 0.023 12 1.8 S_precentral-sup-part 1119 754 1787 2.474 0.437 0.119 0.023 12 1.0 S_suborbital 1152 809 1614 2.355 0.518 0.141 0.034 11 1.7 S_subparietal 2835 1974 4066 2.507 0.585 0.125 0.031 23 4.0 S_temporal_inf 7564 5178 12221 2.547 0.455 0.108 0.021 55 6.4 S_temporal_sup 493 335 571 2.052 0.531 0.117 0.022 5 0.4 S_temporal_transverse #----------------------------------------- #@# Parcellation Stats 2 rh Fri Sep 27 05:39:07 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 290552 Total vertex volume 287212 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1118 743 2020 2.225 0.676 0.146 0.048 19 2.5 G&S_frontomargin 2720 1762 5280 2.586 0.560 0.135 0.036 38 4.0 G&S_occipital_inf 1834 1016 2458 2.213 0.615 0.126 0.043 26 3.6 G&S_paracentral 2157 1265 3776 2.675 0.523 0.117 0.032 28 2.8 G&S_subcentral 1646 1046 3556 2.519 0.555 0.165 0.065 44 4.4 G&S_transv_frontopol 4079 2819 7545 2.498 0.606 0.130 0.028 51 4.9 G&S_cingul-Ant 1730 1229 3350 2.522 0.596 0.120 0.020 16 1.4 G&S_cingul-Mid-Ant 1762 1191 3140 2.602 0.458 0.122 0.030 15 2.2 G&S_cingul-Mid-Post 969 604 1956 2.686 0.675 0.147 0.053 16 1.8 G_cingul-Post-dorsal 489 294 977 2.548 0.580 0.126 0.043 6 0.7 G_cingul-Post-ventral 3393 2059 3809 1.750 0.429 0.142 0.042 48 6.2 G_cuneus 1424 877 3517 3.023 0.399 0.116 0.026 15 1.4 G_front_inf-Opercular 479 308 1045 2.694 0.449 0.136 0.028 6 0.6 G_front_inf-Orbital 1477 874 2893 2.550 0.487 0.144 0.050 26 3.0 G_front_inf-Triangul 5300 3318 11484 2.625 0.538 0.135 0.037 85 8.2 G_front_middle 8501 5409 19284 2.723 0.628 0.133 0.041 139 14.6 G_front_sup 968 586 1765 2.726 0.635 0.118 0.062 18 2.7 G_Ins_lg&S_cent_ins 953 518 2163 3.037 0.808 0.136 0.065 22 2.5 G_insular_short 3256 2000 5832 2.370 0.560 0.134 0.038 46 5.0 G_occipital_middle 2082 1244 2906 2.014 0.474 0.121 0.029 23 2.6 G_occipital_sup 3368 2127 6435 2.492 0.577 0.133 0.042 54 6.0 G_oc-temp_lat-fusifor 4302 2820 6211 1.970 0.554 0.151 0.046 70 8.4 G_oc-temp_med-Lingual 1300 818 3329 2.945 0.934 0.114 0.041 14 2.3 G_oc-temp_med-Parahip 3640 2182 7184 2.577 0.576 0.137 0.046 68 7.5 G_orbital 3858 2369 7205 2.478 0.553 0.139 0.038 62 5.7 G_pariet_inf-Angular 3451 1992 6293 2.575 0.580 0.116 0.041 55 6.0 G_pariet_inf-Supramar 2949 1763 4573 2.108 0.548 0.112 0.031 35 3.4 G_parietal_sup 3195 1673 4198 2.105 0.596 0.122 0.041 55 5.0 G_postcentral 3685 1872 5821 2.577 0.649 0.104 0.033 44 5.0 G_precentral 3553 2172 6169 2.363 0.587 0.136 0.048 63 7.4 G_precuneus 1114 683 1892 2.024 0.641 0.126 0.049 20 2.3 G_rectus 498 296 871 2.513 1.064 0.069 0.031 4 0.4 G_subcallosal 600 339 892 2.152 0.695 0.116 0.044 13 1.1 G_temp_sup-G_T_transv 2821 1662 6708 3.101 0.671 0.126 0.036 41 4.2 G_temp_sup-Lateral 1522 1021 3155 3.091 1.097 0.115 0.038 19 2.7 G_temp_sup-Plan_polar 1191 716 1693 2.228 0.461 0.092 0.028 9 1.3 G_temp_sup-Plan_tempo 2757 1773 6153 2.690 0.665 0.139 0.046 52 5.1 G_temporal_inf 4034 2541 10081 2.920 0.570 0.136 0.037 72 5.5 G_temporal_middle 460 326 587 2.217 0.457 0.092 0.015 2 0.2 Lat_Fis-ant-Horizont 203 139 284 2.575 0.498 0.131 0.018 1 0.2 Lat_Fis-ant-Vertical 1772 1266 2444 2.280 0.469 0.128 0.029 16 2.1 Lat_Fis-post 4878 3291 6335 1.855 0.478 0.154 0.044 73 8.7 Pole_occipital 1983 1303 6659 3.522 0.669 0.130 0.031 25 2.4 Pole_temporal 2991 2394 4001 1.888 0.547 0.160 0.048 47 6.9 S_calcarine 3210 2356 3682 1.777 0.573 0.119 0.027 23 4.1 S_central 1705 1138 2237 2.096 0.430 0.119 0.027 16 1.7 S_cingul-Marginalis 581 417 998 2.846 0.413 0.103 0.017 2 0.4 S_circular_insula_ant 1581 1103 2558 2.817 0.670 0.109 0.024 13 1.6 S_circular_insula_inf 1795 1240 2931 2.833 0.399 0.103 0.019 9 1.5 S_circular_insula_sup 920 658 1791 2.890 0.687 0.121 0.032 8 1.1 S_collat_transv_ant 931 648 1307 2.299 0.409 0.130 0.031 9 1.0 S_collat_transv_post 2754 1858 4052 2.289 0.426 0.110 0.021 22 2.4 S_front_inf 3620 2436 5638 2.283 0.573 0.120 0.029 39 4.4 S_front_middle 3589 2436 6053 2.476 0.490 0.110 0.024 28 3.7 S_front_sup 672 467 984 2.259 0.387 0.106 0.032 5 0.9 S_interm_prim-Jensen 4466 3010 6228 2.128 0.488 0.115 0.023 38 4.3 S_intrapariet&P_trans 989 681 1119 1.958 0.338 0.121 0.021 8 0.8 S_oc_middle&Lunatus 1510 1049 1932 2.084 0.405 0.124 0.024 12 1.6 S_oc_sup&transversal 1565 1072 2219 2.301 0.505 0.124 0.025 12 1.6 S_occipital_ant 1725 1149 2648 2.505 0.534 0.121 0.027 20 1.9 S_oc-temp_lat 2527 1824 3582 2.276 0.454 0.115 0.021 20 2.1 S_oc-temp_med&Lingual 638 449 961 2.124 0.447 0.134 0.029 7 0.9 S_orbital_lateral 797 564 1071 2.230 0.790 0.105 0.016 5 0.5 S_orbital_med-olfact 1708 1104 2790 2.505 0.526 0.127 0.039 23 2.8 S_orbital-H_Shaped 3694 2410 4419 2.035 0.515 0.119 0.026 33 3.9 S_parieto_occipital 1296 850 1130 1.793 0.710 0.158 0.034 33 1.6 S_pericallosal 3160 2116 4037 2.150 0.417 0.110 0.024 24 3.0 S_postcentral 2006 1366 2756 2.419 0.401 0.108 0.020 12 1.6 S_precentral-inf-part 1817 1151 2413 2.303 0.463 0.108 0.026 13 2.0 S_precentral-sup-part 472 339 642 2.351 0.556 0.136 0.022 5 0.4 S_suborbital 1814 1215 2947 2.434 0.466 0.139 0.036 22 2.4 S_subparietal 1479 1020 2063 2.587 0.593 0.119 0.018 11 1.4 S_temporal_inf 8600 5928 13608 2.500 0.498 0.107 0.021 60 7.1 S_temporal_sup 363 259 490 2.258 0.547 0.126 0.031 3 0.4 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Sep 27 05:39:43 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL lh ../surf/lh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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... 1569 labels changed using aseg relabeling using gibbs priors... 000: 2212 changed, 177022 examined... 001: 525 changed, 10380 examined... 002: 132 changed, 2934 examined... 003: 48 changed, 792 examined... 004: 21 changed, 286 examined... 005: 10 changed, 114 examined... 006: 10 changed, 75 examined... 007: 8 changed, 72 examined... 008: 6 changed, 48 examined... 009: 6 changed, 43 examined... 010: 5 changed, 34 examined... 011: 6 changed, 37 examined... 012: 8 changed, 32 examined... 013: 8 changed, 45 examined... 014: 6 changed, 45 examined... 015: 3 changed, 31 examined... 016: 4 changed, 20 examined... 017: 4 changed, 26 examined... 018: 1 changed, 29 examined... 019: 0 changed, 6 examined... 216 labels changed using aseg 000: 63 total segments, 30 labels (178 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... 1334 vertices marked for relabeling... 1334 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 13 seconds. #----------------------------------------- #@# Cortical Parc 3 rh Fri Sep 27 05:39:56 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 BIO-ALS-701-088-BL rh ../surf/rh.sphere.reg /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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... 1367 labels changed using aseg relabeling using gibbs priors... 000: 2663 changed, 177054 examined... 001: 617 changed, 12094 examined... 002: 174 changed, 3517 examined... 003: 69 changed, 976 examined... 004: 42 changed, 405 examined... 005: 21 changed, 232 examined... 006: 14 changed, 112 examined... 007: 9 changed, 77 examined... 008: 7 changed, 47 examined... 009: 4 changed, 35 examined... 010: 7 changed, 26 examined... 011: 4 changed, 29 examined... 012: 5 changed, 22 examined... 013: 4 changed, 25 examined... 014: 4 changed, 24 examined... 015: 4 changed, 22 examined... 016: 4 changed, 22 examined... 017: 2 changed, 18 examined... 018: 0 changed, 10 examined... 343 labels changed using aseg 000: 68 total segments, 33 labels (392 vertices) changed 001: 38 total segments, 3 labels (4 vertices) changed 002: 35 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 9 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 853 vertices marked for relabeling... 853 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 14 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Sep 27 05:40:10 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 287758 Total vertex volume 285088 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 2070 1382 3884 2.602 0.687 0.138 0.025 30 2.2 caudalanteriorcingulate 4761 3067 7942 2.514 0.529 0.118 0.031 59 6.3 caudalmiddlefrontal 5120 3335 5917 1.792 0.485 0.140 0.037 60 7.9 cuneus 356 253 1343 3.951 0.620 0.120 0.031 3 0.4 entorhinal 4269 2850 7351 2.447 0.509 0.115 0.027 42 4.4 fusiform 8674 5822 14265 2.312 0.483 0.133 0.032 103 11.3 inferiorparietal 6609 4400 14019 2.725 0.748 0.140 0.040 105 11.1 inferiortemporal 1809 1163 2976 2.420 0.877 0.132 0.039 27 2.5 isthmuscingulate 10359 6777 15867 2.189 0.553 0.140 0.036 147 16.2 lateraloccipital 5794 3737 10261 2.488 0.698 0.134 0.041 81 10.6 lateralorbitofrontal 5808 3983 8346 1.987 0.532 0.145 0.039 82 8.9 lingual 2988 1904 4878 2.216 0.760 0.120 0.039 47 4.3 medialorbitofrontal 10235 6657 20535 2.730 0.656 0.125 0.036 145 16.3 middletemporal 1265 882 2556 2.516 0.740 0.099 0.035 17 1.9 parahippocampal 3281 1998 5001 2.338 0.527 0.116 0.032 34 4.4 paracentral 2459 1606 4821 2.776 0.478 0.111 0.029 23 2.6 parsopercularis 1194 794 2358 2.649 0.447 0.141 0.033 18 1.5 parsorbitalis 2800 1806 4900 2.452 0.541 0.117 0.027 27 2.8 parstriangularis 2703 2108 2808 1.517 0.468 0.174 0.051 44 6.7 pericalcarine 9069 5569 12097 2.080 0.597 0.116 0.033 97 11.9 postcentral 2581 1641 4182 2.376 0.845 0.139 0.035 40 3.2 posteriorcingulate 9435 5592 14241 2.488 0.637 0.116 0.034 157 14.0 precentral 7130 4811 11578 2.296 0.567 0.133 0.036 82 10.1 precuneus 1996 1331 3863 2.716 0.690 0.134 0.031 29 2.4 rostralanteriorcingulate 9910 6468 16555 2.295 0.538 0.130 0.031 122 12.0 rostralmiddlefrontal 15564 10399 30066 2.511 0.620 0.128 0.032 190 20.5 superiorfrontal 8543 5468 12102 2.049 0.496 0.121 0.029 93 9.7 superiorparietal 9967 6375 20131 2.821 0.692 0.109 0.028 100 11.8 superiortemporal 7197 4513 11522 2.479 0.581 0.130 0.039 97 11.0 supramarginal 1076 647 1369 2.000 0.530 0.134 0.049 19 2.5 transversetemporal 3711 2475 7358 2.966 0.717 0.119 0.033 48 4.9 insula #----------------------------------------- #@# Parcellation Stats 3 rh Fri Sep 27 05:40:45 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 290552 Total vertex volume 287212 (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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1074 725 1852 2.391 0.525 0.144 0.022 18 1.0 caudalanteriorcingulate 3979 2608 7744 2.604 0.536 0.114 0.028 42 4.4 caudalmiddlefrontal 4501 2829 5055 1.781 0.412 0.136 0.034 53 6.8 cuneus 405 265 1493 3.798 0.807 0.105 0.022 3 0.3 entorhinal 6020 3992 10800 2.520 0.564 0.130 0.037 82 9.0 fusiform 10250 6684 17584 2.383 0.551 0.127 0.030 119 12.4 inferiorparietal 6092 4019 12557 2.743 0.682 0.129 0.035 84 8.7 inferiortemporal 1936 1270 3230 2.309 0.729 0.139 0.044 30 3.2 isthmuscingulate 11334 7413 17023 2.179 0.551 0.137 0.036 144 16.7 lateraloccipital 5633 3577 9753 2.462 0.669 0.141 0.049 100 12.3 lateralorbitofrontal 6263 4293 9114 2.019 0.500 0.150 0.044 94 11.6 lingual 2623 1696 4376 2.201 0.732 0.119 0.039 39 4.1 medialorbitofrontal 8301 5492 17639 2.808 0.589 0.119 0.027 97 8.4 middletemporal 1333 898 2419 2.429 0.662 0.103 0.031 11 1.8 parahippocampal 3297 1890 4467 2.311 0.537 0.123 0.043 41 6.1 paracentral 2608 1663 4949 2.730 0.486 0.110 0.023 22 2.3 parsopercularis 1331 785 2414 2.631 0.497 0.115 0.031 15 1.6 parsorbitalis 2755 1807 4893 2.423 0.481 0.135 0.037 38 4.3 parstriangularis 3202 2423 3462 1.554 0.419 0.163 0.045 52 6.3 pericalcarine 8551 5226 11585 2.109 0.621 0.113 0.031 102 10.5 postcentral 2319 1551 3821 2.368 0.693 0.147 0.041 39 3.4 posteriorcingulate 8805 5297 13459 2.464 0.616 0.113 0.030 84 11.7 precentral 8750 5588 13292 2.269 0.538 0.128 0.038 116 14.4 precuneus 1123 733 1737 2.522 0.744 0.105 0.019 11 0.8 rostralanteriorcingulate 9303 6087 16211 2.397 0.524 0.128 0.031 120 12.0 rostralmiddlefrontal 17285 11571 35804 2.591 0.620 0.129 0.035 243 25.3 superiorfrontal 8138 5159 11499 2.082 0.481 0.114 0.028 84 8.9 superiorparietal 9794 6225 19809 2.878 0.753 0.112 0.030 103 11.9 superiortemporal 6757 4156 10551 2.406 0.532 0.112 0.032 83 9.0 supramarginal 667 406 1021 2.165 0.686 0.130 0.042 15 1.2 transversetemporal 4017 2687 7600 2.928 0.628 0.126 0.042 53 7.2 insula #----------------------------------------- #@# WM/GM Contrast lh Fri Sep 27 05:41:17 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts pctsurfcon --s BIO-ALS-701-088-BL --lh-only Log file is /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts/pctsurfcon.log Fri Sep 27 05:41:17 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 mri_vol2surf --mov /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.wm.mgh --regheader BIO-ALS-701-088-BL --cortex srcvol = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99863 -0.00000 -0.05234 0.00000; -0.05234 0.00000 0.99863 -0.00003; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label Reading surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 = 95946 Masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label Writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.wm.mgh Dim: 177022 1 1 mri_vol2surf --mov /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.gm.mgh --projfrac 0.3 --regheader BIO-ALS-701-088-BL --cortex srcvol = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99863 -0.00000 -0.05234 0.00000; -0.05234 0.00000 0.99863 -0.00003; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label Reading surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 = 112779 Masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.cortex.label Writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.gm.mgh Dim: 177022 1 1 mri_concat /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.wm.mgh /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12774/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh --annot BIO-ALS-701-088-BL lh aparc --sum /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh --annot BIO-ALS-701-088-BL lh aparc --sum /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/stats/lh.w-g.pct.stats --snr sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh Vertex Area is 0.653477 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 #----------------------------------------- #@# WM/GM Contrast rh Fri Sep 27 05:41:23 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts pctsurfcon --s BIO-ALS-701-088-BL --rh-only Log file is /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts/pctsurfcon.log Fri Sep 27 05:41:23 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/pctsurfcon $Id: pctsurfcon,v 1.15 2016/02/12 21:43:15 zkaufman Exp $ Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 mri_vol2surf --mov /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.wm.mgh --regheader BIO-ALS-701-088-BL --cortex srcvol = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99863 -0.00000 -0.05234 0.00000; -0.05234 0.00000 0.99863 -0.00003; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label Reading surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 = 95113 Masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label Writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.wm.mgh Dim: 177054 1 1 mri_vol2surf --mov /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.gm.mgh --projfrac 0.3 --regheader BIO-ALS-701-088-BL --cortex srcvol = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/orig.mgz as target reference. -------- original matrix ----------- -0.99863 -0.00000 -0.05234 0.00000; -0.05234 0.00000 0.99863 -0.00003; 0.00000 -1.00000 0.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label Reading surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 = 112783 Masking with /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.cortex.label Writing to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.gm.mgh Dim: 177054 1 1 mri_concat /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.wm.mgh /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/tmp.pctsurfcon.12835/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh --annot BIO-ALS-701-088-BL rh aparc --sum /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh --annot BIO-ALS-701-088-BL rh aparc --sum /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/stats/rh.w-g.pct.stats --snr sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh Vertex Area is 0.648786 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 Fri Sep 27 05:41:30 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 4710 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 4790 voxels changed to hypointensity... 8907 hypointense voxels neighboring cortex changed #----------------------------------------- #@# AParc-to-ASeg aparc Fri Sep 27 05:41:50 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_aparc2aseg --s BIO-ALS-701-088-BL --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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: /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects subject BIO-ALS-701-088-BL outvol /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading lh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial Loading lh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading rh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial Loading rh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 8.17 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 70 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 85 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 28 rescaling Fourth_Ventricle from 22 --> 18 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 40 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 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 = 567668 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 237 changed. pass 2: 14 changed. pass 3: 5 changed. pass 4: 2 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aparc+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg a2009s Fri Sep 27 05:45:34 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_aparc2aseg --s BIO-ALS-701-088-BL --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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: /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects subject BIO-ALS-701-088-BL outvol /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading lh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial Loading lh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2008.txt) Reading rh white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading rh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial Loading rh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 8.17 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 70 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 85 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 28 rescaling Fourth_Ventricle from 22 --> 18 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 40 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 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 = 567712 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 237 changed. pass 2: 14 changed. pass 3: 5 changed. pass 4: 2 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# AParc-to-ASeg DKTatlas Fri Sep 27 05:49:18 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_aparc2aseg --s BIO-ALS-701-088-BL --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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: /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/RB_all_2016-05-10.vc700.gca label intensities: mri/aseg.auto_noCCseg.label_intensities.txt SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects subject BIO-ALS-701-088-BL outvol mri/aparc.DKTatlas+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading lh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial Loading lh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading rh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial Loading rh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 8.17 reading 47 labels from mri/aseg.auto_noCCseg.label_intensities.txt rescaling Left_Cerebral_White_Matter from 107 --> 104 rescaling Left_Cerebral_Cortex from 61 --> 70 rescaling Left_Lateral_Ventricle from 13 --> 16 rescaling Left_Inf_Lat_Vent from 34 --> 34 rescaling Left_Cerebellum_White_Matter from 86 --> 90 rescaling Left_Cerebellum_Cortex from 60 --> 62 rescaling Left_Thalamus from 94 --> 101 rescaling Left_Thalamus_Proper from 84 --> 95 rescaling Left_Caudate from 75 --> 85 rescaling Left_Putamen from 80 --> 92 rescaling Left_Pallidum from 98 --> 101 rescaling Third_Ventricle from 25 --> 28 rescaling Fourth_Ventricle from 22 --> 18 rescaling Brain_Stem from 81 --> 84 rescaling Left_Hippocampus from 57 --> 72 rescaling Left_Amygdala from 56 --> 76 rescaling CSF from 32 --> 40 rescaling Left_Accumbens_area from 62 --> 68 rescaling Left_VentralDC from 87 --> 92 rescaling Right_Cerebral_White_Matter from 105 --> 104 rescaling Right_Cerebral_Cortex from 58 --> 74 rescaling Right_Lateral_Ventricle from 13 --> 14 rescaling Right_Inf_Lat_Vent from 25 --> 28 rescaling Right_Cerebellum_White_Matter from 87 --> 88 rescaling Right_Cerebellum_Cortex from 59 --> 66 rescaling Right_Thalamus_Proper from 85 --> 85 rescaling Right_Caudate from 62 --> 80 rescaling Right_Putamen from 80 --> 86 rescaling Right_Pallidum from 97 --> 93 rescaling Right_Hippocampus from 53 --> 69 rescaling Right_Amygdala from 55 --> 73 rescaling Right_Accumbens_area from 65 --> 78 rescaling Right_VentralDC from 86 --> 91 rescaling Fifth_Ventricle from 40 --> 36 rescaling WM_hypointensities from 78 --> 76 rescaling non_WM_hypointensities from 40 --> 44 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 = 567712 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 237 changed. pass 2: 14 changed. pass 3: 5 changed. pass 4: 2 changed. pass 5: 0 changed. nchanged = 0 Writing output aseg to mri/aparc.DKTatlas+aseg.mgz #----------------------------------------- #@# APas-to-ASeg Fri Sep 27 05:53:02 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri apas2aseg --i aparc+aseg.mgz --o aseg.mgz Fri Sep 27 05:53:02 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/apas2aseg --i aparc+aseg.mgz --o aseg.mgz freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c $Id: apas2aseg,v 1.2 2016/02/12 21:43:14 zkaufman Exp $ Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 aura.nmr.mgh.harvard.edu machine x86_64 user mn457 input aparc+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output aseg.mgz Binarizing based on threshold min -infinity max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Replacing 72 1: 1000 3 2: 2000 42 3: 1001 3 4: 2001 42 5: 1002 3 6: 2002 42 7: 1003 3 8: 2003 42 9: 1004 3 10: 2004 42 11: 1005 3 12: 2005 42 13: 1006 3 14: 2006 42 15: 1007 3 16: 2007 42 17: 1008 3 18: 2008 42 19: 1009 3 20: 2009 42 21: 1010 3 22: 2010 42 23: 1011 3 24: 2011 42 25: 1012 3 26: 2012 42 27: 1013 3 28: 2013 42 29: 1014 3 30: 2014 42 31: 1015 3 32: 2015 42 33: 1016 3 34: 2016 42 35: 1017 3 36: 2017 42 37: 1018 3 38: 2018 42 39: 1019 3 40: 2019 42 41: 1020 3 42: 2020 42 43: 1021 3 44: 2021 42 45: 1022 3 46: 2022 42 47: 1023 3 48: 2023 42 49: 1024 3 50: 2024 42 51: 1025 3 52: 2025 42 53: 1026 3 54: 2026 42 55: 1027 3 56: 2027 42 57: 1028 3 58: 2028 42 59: 1029 3 60: 2029 42 61: 1030 3 62: 2030 42 63: 1031 3 64: 2031 42 65: 1032 3 66: 2032 42 67: 1033 3 68: 2033 42 69: 1034 3 70: 2034 42 71: 1035 3 72: 2035 42 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done Started at Fri Sep 27 05:53:02 EDT 2019 Ended at Fri Sep 27 05:53:07 EDT 2019 Apas2aseg-Run-Time-Sec 5 apas2aseg Done #-------------------------------------------- #@# ASeg Stats Fri Sep 27 05:53:07 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL 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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/ASegStatsLUT.txt --subject BIO-ALS-701-088-BL $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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/ASegStatsLUT.txt --subject BIO-ALS-701-088-BL sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 atlas_icv (eTIV) = 1890020 mm^3 (det: 1.030733 ) Computing euler number orig.nofix lheno = -168, rheno = -160 orig.nofix lhholes = 85, rhholes = 81 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done #----------------------------------------- #@# WMParc Fri Sep 27 05:54:55 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL mri_aparc2aseg --s BIO-ALS-701-088-BL --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects subject BIO-ALS-701-088-BL outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aparc+aseg.mgz Reading lh white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading lh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial Loading lh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading rh pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial Loading rh annotations from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/ribbon.mgz Loading filled from /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/ribbon.mgz Ripping vertices labeled as unkown Ripped 8320 vertices from left hemi Ripped 8601 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/aseg.mgz Loading Ctx Seg File /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 = 1185124 Used brute-force search on 323 voxels Fixing Parahip LH WM Found 14 clusters 0 k 2090.000000 1 k 1.000000 2 k 133.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 1.000000 8 k 1.000000 9 k 2.000000 10 k 3.000000 11 k 1.000000 12 k 3.000000 13 k 1.000000 Fixing Parahip RH WM Found 10 clusters 0 k 1.000000 1 k 3.000000 2 k 5.000000 3 k 3.000000 4 k 13.000000 5 k 1.000000 6 k 1.000000 7 k 1943.000000 8 k 1.000000 9 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 BIO-ALS-701-088-BL --surf-wm-vol --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 BIO-ALS-701-088-BL --surf-wm-vol --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/WMParcStatsLUT.txt --etiv sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 UseRobust 0 atlas_icv (eTIV) = 1890020 mm^3 (det: 1.030733 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label #-------------------------------------------- #@# BA_exvivo Labels lh Fri Sep 27 06:03:42 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA1_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 770 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4899 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA2_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 1488 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 9397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3a_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 179 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4256 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3b_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 747 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6730 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4a_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 934 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 6718 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4p_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 351 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4421 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA6_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 2957 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 16546 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA44_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 687 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4868 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA45_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 1408 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4830 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V1_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 3260 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 7901 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V2_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 5882 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 13996 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.MT_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 924 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2942 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1324 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 50 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1249 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 194 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1208 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 465 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2557 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 76 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1580 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 120 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2116 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 387 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2706 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1644 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 1358 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 8393 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 251 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 2163 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 396 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 2330 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 5735 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 2792 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 6126 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 282 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 795 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 11 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 481 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177022 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 460 mri_label2label: Done mris_label2annot --s BIO-ALS-701-088-BL --hemi lh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label cmdline mris_label2annot --s BIO-ALS-701-088-BL --hemi lh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu machine x86_64 user mn457 subject BIO-ALS-701-088-BL hemi lh SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects ColorTable /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 123126 unhit vertices Writing annot to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/lh.BA_exvivo.annot mris_label2annot --s BIO-ALS-701-088-BL --hemi lh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label cmdline mris_label2annot --s BIO-ALS-701-088-BL --hemi lh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu machine x86_64 user mn457 subject BIO-ALS-701-088-BL hemi lh SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects ColorTable /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 145602 unhit vertices Writing annot to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 287758 Total vertex volume 285088 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1505 779 1976 2.111 0.589 0.124 0.047 20 2.5 BA1_exvivo 5483 3443 7510 2.134 0.493 0.119 0.030 62 6.3 BA2_exvivo 1160 823 1074 1.629 0.387 0.145 0.031 13 1.6 BA3a_exvivo 2727 1768 3186 1.781 0.548 0.114 0.033 27 3.7 BA3b_exvivo 2169 1207 3193 2.456 0.600 0.117 0.042 86 3.7 BA4a_exvivo 1400 958 2175 2.400 0.578 0.112 0.029 9 1.9 BA4p_exvivo 12472 7585 22371 2.614 0.645 0.117 0.033 134 17.7 BA6_exvivo 2794 1809 5444 2.746 0.503 0.112 0.027 27 2.9 BA44_exvivo 3909 2499 6793 2.369 0.560 0.122 0.030 42 4.3 BA45_exvivo 4976 3742 5861 1.583 0.497 0.166 0.048 77 11.5 V1_exvivo 11439 7461 15284 1.986 0.525 0.147 0.041 167 19.9 V2_exvivo 2782 1866 4708 2.302 0.524 0.128 0.027 37 2.9 MT_exvivo 484 324 1513 3.612 0.796 0.104 0.030 4 0.6 perirhinal_exvivo 596 427 1284 2.936 0.928 0.114 0.024 5 0.6 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 BIO-ALS-701-088-BL lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 287758 Total vertex volume 285088 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 968 483 1254 2.069 0.620 0.135 0.040 14 1.7 BA1_exvivo 2158 1297 3335 2.299 0.474 0.104 0.022 17 1.9 BA2_exvivo 1005 713 856 1.591 0.345 0.149 0.032 12 1.4 BA3a_exvivo 1530 1036 1495 1.481 0.310 0.100 0.023 10 1.4 BA3b_exvivo 2086 1162 2960 2.437 0.592 0.111 0.041 83 3.4 BA4a_exvivo 1093 800 1692 2.321 0.578 0.119 0.030 7 1.5 BA4p_exvivo 6994 4190 11709 2.515 0.654 0.117 0.033 70 10.1 BA6_exvivo 1683 1095 3503 2.757 0.453 0.115 0.030 19 1.9 BA44_exvivo 1377 875 2732 2.504 0.593 0.121 0.031 14 1.6 BA45_exvivo 5300 3943 6454 1.597 0.516 0.169 0.051 90 12.9 V1_exvivo 5912 3899 7582 1.933 0.532 0.150 0.040 83 10.0 V2_exvivo 780 517 1400 2.437 0.588 0.130 0.029 11 0.9 MT_exvivo 233 151 888 3.780 0.782 0.098 0.026 2 0.3 perirhinal_exvivo 301 212 647 3.240 0.643 0.107 0.026 2 0.3 entorhinal_exvivo #-------------------------------------------- #@# BA_exvivo Labels rh Fri Sep 27 06:08:24 EDT 2019 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA1_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 749 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4711 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA2_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 995 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 7682 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3a_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 197 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4177 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3b_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 497 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 5019 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4a_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 1179 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6926 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4p_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 400 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4873 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA6_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 2297 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 14553 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA44_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 1492 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 8404 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA45_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 1777 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 7132 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V1_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 3425 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 8152 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V2_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 6140 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 14156 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.MT_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 1602 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 3534 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 78 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1116 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 822 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 162 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 1038 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 468 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 3156 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 67 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1765 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 203 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2386 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 263 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1651 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1585 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 1364 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 8323 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 95 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1107 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 423 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1601 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 2313 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 5545 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 2960 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 6397 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 254 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 522 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 45 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 739 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject BIO-ALS-701-088-BL --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = BIO-ALS-701-088-BL 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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white Reading target registration /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 177054 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 314 mri_label2label: Done mris_label2annot --s BIO-ALS-701-088-BL --hemi rh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label cmdline mris_label2annot --s BIO-ALS-701-088-BL --hemi rh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu machine x86_64 user mn457 subject BIO-ALS-701-088-BL hemi rh SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects ColorTable /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 123813 unhit vertices Writing annot to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label/rh.BA_exvivo.annot mris_label2annot --s BIO-ALS-701-088-BL --hemi rh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/label cmdline mris_label2annot --s BIO-ALS-701-088-BL --hemi rh --ctab /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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 aura.nmr.mgh.harvard.edu machine x86_64 user mn457 subject BIO-ALS-701-088-BL hemi rh SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects ColorTable /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 147410 unhit vertices Writing annot to /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/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 BIO-ALS-701-088-BL rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 290552 Total vertex volume 287212 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 1214 630 1674 2.173 0.606 0.127 0.041 17 2.2 BA1_exvivo 4267 2632 5889 2.233 0.463 0.109 0.029 49 4.6 BA2_exvivo 1146 882 1094 1.608 0.362 0.145 0.034 12 1.8 BA3a_exvivo 2292 1386 2405 1.646 0.570 0.107 0.027 22 2.7 BA3b_exvivo 2128 1146 3033 2.453 0.596 0.118 0.041 30 3.9 BA4a_exvivo 1355 910 2051 2.282 0.501 0.127 0.041 16 2.6 BA4p_exvivo 9968 6074 17768 2.569 0.624 0.114 0.032 112 13.1 BA6_exvivo 4153 2654 7665 2.705 0.492 0.111 0.022 33 3.9 BA44_exvivo 5432 3438 9620 2.469 0.518 0.128 0.034 68 7.6 BA45_exvivo 5423 3980 6536 1.626 0.439 0.163 0.046 87 10.9 V1_exvivo 11467 7434 15142 1.976 0.483 0.143 0.040 156 19.6 V2_exvivo 3462 2332 5767 2.335 0.486 0.132 0.031 39 4.4 MT_exvivo 552 349 1882 3.679 0.853 0.094 0.023 3 0.4 perirhinal_exvivo 382 261 908 2.984 0.697 0.105 0.018 2 0.3 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 BIO-ALS-701-088-BL rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/mri/wm.mgz... reading input surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... reading input pial surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.pial... reading input white surface /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 290552 Total vertex volume 287212 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/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) = 1890020 mm^3 (det: 1.030733 ) lhCtxGM: 282942.698 281997.000 diff= 945.7 pctdiff= 0.334 rhCtxGM: 285433.982 284656.000 diff= 778.0 pctdiff= 0.273 lhCtxWM: 314130.616 314689.000 diff= -558.4 pctdiff=-0.178 rhCtxWM: 304619.984 306098.000 diff=-1478.0 pctdiff=-0.485 SubCortGMVol 69568.000 SupraTentVol 1285607.280 (1281135.000) diff=4472.280 pctdiff=0.348 SupraTentVolNotVent 1261490.280 (1257018.000) diff=4472.280 pctdiff=0.355 BrainSegVol 1451642.000 (1448417.000) diff=3225.000 pctdiff=0.222 BrainSegVolNotVent 1423124.000 (1422719.280) diff=404.720 pctdiff=0.028 BrainSegVolNotVent 1423124.000 CerebellumVol 166014.000 VentChorVol 24117.000 3rd4th5thCSF 4401.000 CSFVol 1176.000, OptChiasmVol 92.000 MaskVol 1951002.000 827 423 1000 2.005 0.629 0.123 0.037 11 1.3 BA1_exvivo 2520 1508 3762 2.294 0.452 0.106 0.033 35 2.9 BA2_exvivo 960 768 924 1.577 0.336 0.148 0.032 10 1.4 BA3a_exvivo 1739 1129 1624 1.459 0.382 0.104 0.023 14 1.7 BA3b_exvivo 1287 741 1797 2.324 0.645 0.126 0.041 14 2.5 BA4a_exvivo 1017 730 1678 2.345 0.474 0.119 0.037 8 1.9 BA4p_exvivo 6630 3960 11237 2.548 0.636 0.113 0.033 79 8.8 BA6_exvivo 868 542 1947 2.978 0.450 0.110 0.019 6 0.7 BA44_exvivo 1428 873 2811 2.540 0.526 0.137 0.046 22 2.8 BA45_exvivo 5135 3820 6128 1.616 0.443 0.165 0.046 83 10.6 V1_exvivo 6153 4021 7702 1.881 0.465 0.149 0.046 90 12.4 V2_exvivo 521 354 756 2.127 0.429 0.136 0.043 6 1.2 MT_exvivo 325 203 1245 3.777 0.846 0.094 0.018 2 0.3 perirhinal_exvivo 234 167 496 3.111 0.614 0.107 0.018 1 0.1 entorhinal_exvivo #-------------------------------------------- #@# Segmentation of brainstem substructures Fri Sep 27 06:13:00 EDT 2019 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/segmentBS.sh /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/MCRv80 /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 BIO-ALS-701-088-BL /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects See log file: /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/scripts/brainstem-structures.log #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Fri Sep 27 06:28:09 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.43426 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.thickness.fsaverage.mris_preproc.log Fri Sep 27 06:28:09 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.43426 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:09 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43426/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.thickness --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43426/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.43426/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.thickness Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.43426/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.43426/BIO-ALS-701-088-BL.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.43426 Fri Sep 27 06:28:15 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area fsaverage Fri Sep 27 06:28:15 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.43551 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.area.fsaverage.mris_preproc.log Fri Sep 27 06:28:15 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.43551 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:15 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43551/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43551/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.43551/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177022) Reverse Loop had 47797 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.43551/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.43551/BIO-ALS-701-088-BL.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.43551 Fri Sep 27 06:28:23 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area.pial fsaverage Fri Sep 27 06:28:23 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.43674 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Fri Sep 27 06:28:23 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.43674 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:23 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43674/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area.pial --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43674/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area.pial --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.43674/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.area.pial Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177022) Reverse Loop had 47797 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.43674/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.43674/BIO-ALS-701-088-BL.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.43674 Fri Sep 27 06:28:31 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh volume fsaverage Fri Sep 27 06:28:31 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.43794 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.volume.fsaverage.mris_preproc.log Fri Sep 27 06:28:31 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.43794 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:31 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43794/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.volume --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43794/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.volume --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.43794/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.volume Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177022) Reverse Loop had 47797 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.43794/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.43794/BIO-ALS-701-088-BL.1.mgh --o lh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.43794 Fri Sep 27 06:28:39 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh curv fsaverage Fri Sep 27 06:28:39 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.43929 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.curv.fsaverage.mris_preproc.log Fri Sep 27 06:28:39 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.43929 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:39 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43929/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.43929/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.43929/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.curv Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.43929/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.43929/BIO-ALS-701-088-BL.1.mgh --o lh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.43929 Fri Sep 27 06:28:45 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh sulc fsaverage Fri Sep 27 06:28:45 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44049 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.sulc.fsaverage.mris_preproc.log Fri Sep 27 06:28:45 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44049 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:45 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44049/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sulc --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44049/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sulc --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44049/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sulc Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44049/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44049/BIO-ALS-701-088-BL.1.mgh --o lh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44049 Fri Sep 27 06:28:51 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh white.K fsaverage Fri Sep 27 06:28:51 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44166 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.white.K.fsaverage.mris_preproc.log Fri Sep 27 06:28:52 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44166 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:52 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44166/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.K --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44166/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.K --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.K srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44166/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.K Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44166/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44166/BIO-ALS-701-088-BL.1.mgh --o lh.white.K.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.white.K.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44166 Fri Sep 27 06:28:58 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh white.H fsaverage Fri Sep 27 06:28:58 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas white.H --target fsaverage --out lh.white.H.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44285 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.white.H.fsaverage.mris_preproc.log Fri Sep 27 06:28:58 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas white.H --target fsaverage --out lh.white.H.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44285 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:28:58 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44285/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.H --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44285/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.H --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.H srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44285/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.white.H Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44285/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44285/BIO-ALS-701-088-BL.1.mgh --o lh.white.H.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.white.H.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44285 Fri Sep 27 06:29:04 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh jacobian_white fsaverage Fri Sep 27 06:29:04 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44402 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.jacobian_white.fsaverage.mris_preproc.log Fri Sep 27 06:29:04 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44402 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:04 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44402/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.jacobian_white --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44402/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.jacobian_white --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44402/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.jacobian_white Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44402/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44402/BIO-ALS-701-088-BL.1.mgh --o lh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44402 Fri Sep 27 06:29:11 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh w-g.pct.mgh fsaverage Fri Sep 27 06:29:11 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44519 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is lh.w-g.pct.mgh.fsaverage.mris_preproc.log Fri Sep 27 06:29:11 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44519 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:11 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44519/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44519/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44519/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/lh.w-g.pct.mgh Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177022) Reverse Loop had 47797 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 130267, nTrgMulti = 33575, MnTrgMultiHits = 2.42359 nSrc121 = 148791, nSrcLost = 0, nSrcMulti = 28231, MnSrcMultiHits = 2.22621 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44519/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44519/BIO-ALS-701-088-BL.1.mgh --o lh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44519 Fri Sep 27 06:29:17 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh thickness fsaverage Fri Sep 27 06:29:17 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.44638 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.thickness.fsaverage.mris_preproc.log Fri Sep 27 06:29:17 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44638 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:17 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44638/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.thickness --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44638/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.thickness --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44638/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.thickness Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44638/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44638/BIO-ALS-701-088-BL.1.mgh --o rh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44638 Fri Sep 27 06:29:23 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh area fsaverage Fri Sep 27 06:29:23 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.44756 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.area.fsaverage.mris_preproc.log Fri Sep 27 06:29:24 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas area --target fsaverage --out rh.area.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44756 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:24 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44756/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44756/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44756/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177054) Reverse Loop had 48177 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44756/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44756/BIO-ALS-701-088-BL.1.mgh --o rh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44756 Fri Sep 27 06:29:31 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh area.pial fsaverage Fri Sep 27 06:29:31 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.44881 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.area.pial.fsaverage.mris_preproc.log Fri Sep 27 06:29:32 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas area.pial --target fsaverage --out rh.area.pial.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.44881 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:32 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44881/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area.pial --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.44881/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area.pial --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.44881/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.area.pial Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177054) Reverse Loop had 48177 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.44881/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.44881/BIO-ALS-701-088-BL.1.mgh --o rh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.44881 Fri Sep 27 06:29:40 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh volume fsaverage Fri Sep 27 06:29:40 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.45009 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.volume.fsaverage.mris_preproc.log Fri Sep 27 06:29:40 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas volume --target fsaverage --out rh.volume.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45009 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:40 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45009/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.volume --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45009/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.volume --jac --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45009/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.volume Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (177054) Reverse Loop had 48177 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45009/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45009/BIO-ALS-701-088-BL.1.mgh --o rh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45009 Fri Sep 27 06:29:48 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh curv fsaverage Fri Sep 27 06:29:48 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45135 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.curv.fsaverage.mris_preproc.log Fri Sep 27 06:29:48 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas curv --target fsaverage --out rh.curv.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45135 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:48 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45135/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45135/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45135/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.curv Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45135/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45135/BIO-ALS-701-088-BL.1.mgh --o rh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45135 Fri Sep 27 06:29:54 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh sulc fsaverage Fri Sep 27 06:29:54 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45255 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.sulc.fsaverage.mris_preproc.log Fri Sep 27 06:29:55 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas sulc --target fsaverage --out rh.sulc.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45255 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:29:55 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45255/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sulc --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45255/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sulc --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45255/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sulc Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45255/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45255/BIO-ALS-701-088-BL.1.mgh --o rh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45255 Fri Sep 27 06:30:01 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh white.K fsaverage Fri Sep 27 06:30:01 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas white.K --target fsaverage --out rh.white.K.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45374 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.white.K.fsaverage.mris_preproc.log Fri Sep 27 06:30:01 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas white.K --target fsaverage --out rh.white.K.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45374 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:30:01 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45374/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.K --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45374/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.K --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.K srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45374/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.K Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45374/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45374/BIO-ALS-701-088-BL.1.mgh --o rh.white.K.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.white.K.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45374 Fri Sep 27 06:30:07 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh white.H fsaverage Fri Sep 27 06:30:07 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas white.H --target fsaverage --out rh.white.H.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45505 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.white.H.fsaverage.mris_preproc.log Fri Sep 27 06:30:07 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas white.H --target fsaverage --out rh.white.H.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45505 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:30:07 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45505/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.H --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45505/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.H --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.H srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45505/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.white.H Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45505/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45505/BIO-ALS-701-088-BL.1.mgh --o rh.white.H.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.white.H.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45505 Fri Sep 27 06:30:14 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh jacobian_white fsaverage Fri Sep 27 06:30:14 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45622 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.jacobian_white.fsaverage.mris_preproc.log Fri Sep 27 06:30:14 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas jacobian_white --target fsaverage --out rh.jacobian_white.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45622 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:30:14 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45622/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.jacobian_white --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45622/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.jacobian_white --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45622/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.jacobian_white Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45622/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45622/BIO-ALS-701-088-BL.1.mgh --o rh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45622 Fri Sep 27 06:30:20 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc rh w-g.pct.mgh fsaverage Fri Sep 27 06:30:20 EDT 2019 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.45740 /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf Log file is rh.w-g.pct.mgh.fsaverage.mris_preproc.log Fri Sep 27 06:30:20 EDT 2019 setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/mris_preproc --s BIO-ALS-701-088-BL --hemi rh --meas w-g.pct.mgh --target fsaverage --out rh.w-g.pct.mgh.fsaverage.mgh Linux aura.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.45740 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 BIO-ALS-701-088-BL Fri Sep 27 06:30:20 EDT 2019 -------------- ----------------------- mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45740/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --srcsubject BIO-ALS-701-088-BL --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.45740/BIO-ALS-701-088-BL.1.mgh --sval /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh --sfmt curv --noreshape --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = BIO-ALS-701-088-BL srcval = /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.45740/BIO-ALS-701-088-BL.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.sphere.reg Loading source data Reading curvature file /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf/rh.w-g.pct.mgh Reading source subject label mask rh.cortex.label masking the input Reading target surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (177054) Reverse Loop had 48177 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 129765, nTrgMulti = 34077, MnTrgMultiHits = 2.41377 nSrc121 = 148380, nSrcLost = 0, nSrcMulti = 28674, MnSrcMultiHits = 2.2194 Reading target space mask label rh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.45740/BIO-ALS-701-088-BL.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.45740/BIO-ALS-701-088-BL.1.mgh --o rh.w-g.pct.mgh.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to rh.w-g.pct.mgh.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.45740 Fri Sep 27 06:30:27 EDT 2019 mris_preproc done #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm0 fsaverage Fri Sep 27 06:30:27 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm5 fsaverage Fri Sep 27 06:30:29 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm10 fsaverage Fri Sep 27 06:30:34 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm15 fsaverage Fri Sep 27 06:30:39 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm20 fsaverage Fri Sep 27 06:30:43 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh thickness fwhm25 fsaverage Fri Sep 27 06:30:48 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm0 fsaverage Fri Sep 27 06:30:53 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm5 fsaverage Fri Sep 27 06:30:56 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm10 fsaverage Fri Sep 27 06:31:00 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm15 fsaverage Fri Sep 27 06:31:04 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm20 fsaverage Fri Sep 27 06:31:09 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area fwhm25 fsaverage Fri Sep 27 06:31:14 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm0 fsaverage Fri Sep 27 06:31:19 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm5 fsaverage Fri Sep 27 06:31:21 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm10 fsaverage Fri Sep 27 06:31:25 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm15 fsaverage Fri Sep 27 06:31:30 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm20 fsaverage Fri Sep 27 06:31:35 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh area.pial fwhm25 fsaverage Fri Sep 27 06:31:39 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm0 fsaverage Fri Sep 27 06:31:44 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm5 fsaverage Fri Sep 27 06:31:47 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm10 fsaverage Fri Sep 27 06:31:51 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm15 fsaverage Fri Sep 27 06:31:55 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm20 fsaverage Fri Sep 27 06:32:00 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh volume fwhm25 fsaverage Fri Sep 27 06:32:04 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm0 fsaverage Fri Sep 27 06:32:09 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm5 fsaverage Fri Sep 27 06:32:12 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm10 fsaverage Fri Sep 27 06:32:16 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm15 fsaverage Fri Sep 27 06:32:20 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm20 fsaverage Fri Sep 27 06:32:25 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh curv fwhm25 fsaverage Fri Sep 27 06:32:29 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm0 fsaverage Fri Sep 27 06:32:35 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm5 fsaverage Fri Sep 27 06:32:37 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm10 fsaverage Fri Sep 27 06:32:41 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm15 fsaverage Fri Sep 27 06:32:46 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm20 fsaverage Fri Sep 27 06:32:51 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh sulc fwhm25 fsaverage Fri Sep 27 06:32:55 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm0 fsaverage Fri Sep 27 06:33:01 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.white.K.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm5 fsaverage Fri Sep 27 06:33:03 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.white.K.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm10 fsaverage Fri Sep 27 06:33:08 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.white.K.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm15 fsaverage Fri Sep 27 06:33:12 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.white.K.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm20 fsaverage Fri Sep 27 06:33:17 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.white.K.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.K fwhm25 fsaverage Fri Sep 27 06:33:22 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.white.K.fsaverage.mgh --tval lh.white.K.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.K.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.white.K.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm0 fsaverage Fri Sep 27 06:33:27 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.white.H.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm5 fsaverage Fri Sep 27 06:33:29 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.white.H.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm10 fsaverage Fri Sep 27 06:33:34 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.white.H.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm15 fsaverage Fri Sep 27 06:33:38 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.white.H.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm20 fsaverage Fri Sep 27 06:33:43 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.white.H.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh white.H fwhm25 fsaverage Fri Sep 27 06:33:48 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.white.H.fsaverage.mgh --tval lh.white.H.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.white.H.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.white.H.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm0 fsaverage Fri Sep 27 06:33:53 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm5 fsaverage Fri Sep 27 06:33:55 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm10 fsaverage Fri Sep 27 06:33:59 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm15 fsaverage Fri Sep 27 06:34:04 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm20 fsaverage Fri Sep 27 06:34:09 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh jacobian_white fwhm25 fsaverage Fri Sep 27 06:34:14 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm0 fsaverage Fri Sep 27 06:34:19 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 0 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label lh.cortex.label masking the input Saving target data Saving to lh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm5 fsaverage Fri Sep 27 06:34:21 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 5 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to lh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm10 fsaverage Fri Sep 27 06:34:25 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 10 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to lh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm15 fsaverage Fri Sep 27 06:34:30 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 15 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 165 Saving target data Saving to lh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm20 fsaverage Fri Sep 27 06:34:34 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 20 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to lh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf lh w-g.pct.mgh fwhm25 fsaverage Fri Sep 27 06:34:39 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 25 --sval lh.w-g.pct.mgh.fsaverage.mgh --tval lh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = lh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/lh.sphere.reg Loading source data Reading source subject label mask lh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label lh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to lh.w-g.pct.mgh.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm0 fsaverage Fri Sep 27 06:34:44 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm5 fsaverage Fri Sep 27 06:34:47 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm10 fsaverage Fri Sep 27 06:34:51 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm15 fsaverage Fri Sep 27 06:34:56 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm20 fsaverage Fri Sep 27 06:35:00 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh thickness fwhm25 fsaverage Fri Sep 27 06:35:05 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.thickness.fsaverage.mgh --tval rh.thickness.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm0 fsaverage Fri Sep 27 06:35:10 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm5 fsaverage Fri Sep 27 06:35:12 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm10 fsaverage Fri Sep 27 06:35:17 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm15 fsaverage Fri Sep 27 06:35:22 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm20 fsaverage Fri Sep 27 06:35:26 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area fwhm25 fsaverage Fri Sep 27 06:35:31 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.area.fsaverage.mgh --tval rh.area.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm0 fsaverage Fri Sep 27 06:35:36 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm5 fsaverage Fri Sep 27 06:35:39 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm10 fsaverage Fri Sep 27 06:35:43 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm15 fsaverage Fri Sep 27 06:35:48 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm20 fsaverage Fri Sep 27 06:35:52 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh area.pial fwhm25 fsaverage Fri Sep 27 06:35:57 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.area.pial.fsaverage.mgh --tval rh.area.pial.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm0 fsaverage Fri Sep 27 06:36:02 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm5 fsaverage Fri Sep 27 06:36:05 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm10 fsaverage Fri Sep 27 06:36:09 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm15 fsaverage Fri Sep 27 06:36:14 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm20 fsaverage Fri Sep 27 06:36:18 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh volume fwhm25 fsaverage Fri Sep 27 06:36:23 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.volume.fsaverage.mgh --tval rh.volume.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm0 fsaverage Fri Sep 27 06:36:28 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm5 fsaverage Fri Sep 27 06:36:30 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm10 fsaverage Fri Sep 27 06:36:35 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm15 fsaverage Fri Sep 27 06:36:39 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm20 fsaverage Fri Sep 27 06:36:44 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh curv fwhm25 fsaverage Fri Sep 27 06:36:48 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.curv.fsaverage.mgh --tval rh.curv.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm0 fsaverage Fri Sep 27 06:36:54 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm5 fsaverage Fri Sep 27 06:36:56 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm10 fsaverage Fri Sep 27 06:37:01 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm15 fsaverage Fri Sep 27 06:37:05 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm20 fsaverage Fri Sep 27 06:37:10 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh sulc fwhm25 fsaverage Fri Sep 27 06:37:15 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.sulc.fsaverage.mgh --tval rh.sulc.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm0 fsaverage Fri Sep 27 06:37:20 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.white.K.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm5 fsaverage Fri Sep 27 06:37:22 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.white.K.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm10 fsaverage Fri Sep 27 06:37:27 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.white.K.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm15 fsaverage Fri Sep 27 06:37:31 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.white.K.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm20 fsaverage Fri Sep 27 06:37:36 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.white.K.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.K fwhm25 fsaverage Fri Sep 27 06:37:41 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.white.K.fsaverage.mgh --tval rh.white.K.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.K.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.K.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.white.K.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm0 fsaverage Fri Sep 27 06:37:46 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.white.H.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm5 fsaverage Fri Sep 27 06:37:48 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.white.H.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm10 fsaverage Fri Sep 27 06:37:53 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.white.H.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm15 fsaverage Fri Sep 27 06:37:57 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.white.H.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm20 fsaverage Fri Sep 27 06:38:02 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.white.H.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh white.H fwhm25 fsaverage Fri Sep 27 06:38:07 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.white.H.fsaverage.mgh --tval rh.white.H.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.white.H.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.white.H.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.white.H.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm0 fsaverage Fri Sep 27 06:38:12 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm5 fsaverage Fri Sep 27 06:38:14 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm10 fsaverage Fri Sep 27 06:38:19 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm15 fsaverage Fri Sep 27 06:38:23 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm20 fsaverage Fri Sep 27 06:38:28 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh jacobian_white fwhm25 fsaverage Fri Sep 27 06:38:33 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.jacobian_white.fsaverage.mgh --tval rh.jacobian_white.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm0 fsaverage Fri Sep 27 06:38:38 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 0 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm0.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Reading target space mask label rh.cortex.label masking the input Saving target data Saving to rh.w-g.pct.mgh.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm5 fsaverage Fri Sep 27 06:38:40 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 5 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm5.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 18 Saving target data Saving to rh.w-g.pct.mgh.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm10 fsaverage Fri Sep 27 06:38:45 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 10 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm10.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 74 Saving target data Saving to rh.w-g.pct.mgh.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm15 fsaverage Fri Sep 27 06:38:49 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 15 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm15.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 166 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 166 Saving target data Saving to rh.w-g.pct.mgh.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm20 fsaverage Fri Sep 27 06:38:54 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 20 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm20.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 294 Saving target data Saving to rh.w-g.pct.mgh.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache surf2surf rh w-g.pct.mgh fwhm25 fsaverage Fri Sep 27 06:38:59 EDT 2019 mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects cd /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/BIO-ALS-701-088-BL/surf mri_surf2surf --prune --s fsaverage --hemi rh --fwhm 25 --sval rh.w-g.pct.mgh.fsaverage.mgh --tval rh.w-g.pct.mgh.fwhm25.fsaverage.mgh --cortex sysname Linux hostname aura.nmr.mgh.harvard.edu machine x86_64 user mn457 srcsubject = fsaverage srcval = rh.w-g.pct.mgh.fsaverage.mgh srctype = trgsubject = fsaverage trgval = rh.w-g.pct.mgh.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = rh.cortex.label label-trg = rh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /autofs/cluster/atassigp/MMMB/MotorNeuronDisease/FS/subjects/fsaverage/surf/rh.sphere.reg Loading source data Reading source subject label mask rh.cortex.label masking the input INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading target space mask label rh.cortex.label Pruning output smoothing mask by thr: 1.175494e-38 NN smoothing output with n = 460 Saving target data Saving to rh.w-g.pct.mgh.fwhm25.fsaverage.mgh Started at Thu Sep 26 18:01:31 EDT 2019 Ended at Fri Sep 27 06:39:05 EDT 2019 #@#%# recon-all-run-time-hours 12.626 recon-all -s BIO-ALS-701-088-BL finished without error at Fri Sep 27 06:39:05 EDT 2019