Mon Oct 13 13:45:36 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 /usr/local/freesurfer/bin/recon-all -s Andre_v_5_3 -i test_output_Andre/T1/T1.nii -all subjid Andre_v_5_3 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux psyk-stud141.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 49416392 35655416 13760976 0 343432 31668980 -/+ buffers/cache: 3643004 45773388 Swap: 10485756 0 10485756 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/13-11:45:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: evaghi Machine: psyk-stud141.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/T1/T1.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/001.mgz mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/T1/T1.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/T1/T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Oct 13 13:45:43 CEST 2014 Found 1 runs /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/001.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz --conform mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) Original Data has (1, 1, 0.999855) mm size and (256, 256, 184) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz... mri_add_xform_to_header -c /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/talairach.xfm /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 13 13:45:57 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 13 13:47:24 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3662, pval=0.0406 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/talairach_avi.log tal_QC_AZS /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/talairach_avi.log TalAviQA: 0.95615 z-score: -4 #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 13 13:47:24 CEST 2014 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux psyk-stud141.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 13 13:47:25 CEST 2014 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.61624 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.61624/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.61624/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-08, -8.3819e-08) j_ras = (6.14673e-08, -5.52391e-08, -1) k_ras = (2.2538e-07, 1, 1.83936e-08) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.61624/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Oct 13 13:47:27 CEST 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.61624/nu0.mnc ./tmp.mri_nu_correct.mni.61624/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.61624/0/ [evaghi@psyk-stud141.uio.no:/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/] [2014-10-13 13:47:27] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.61624/0/ ./tmp.mri_nu_correct.mni.61624/nu0.mnc ./tmp.mri_nu_correct.mni.61624/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 17 CV of field change: 0.000966007 [evaghi@psyk-stud141.uio.no:/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/] [2014-10-13 13:47:41] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.61624/nu0.mnc ./tmp.mri_nu_correct.mni.61624/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Oct 13 13:47:47 CEST 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.61624/nu1.mnc ./tmp.mri_nu_correct.mni.61624/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.61624/1/ [evaghi@psyk-stud141.uio.no:/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/] [2014-10-13 13:47:47] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.61624/1/ ./tmp.mri_nu_correct.mni.61624/nu1.mnc ./tmp.mri_nu_correct.mni.61624/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 15 CV of field change: 0.000955749 [evaghi@psyk-stud141.uio.no:/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/] [2014-10-13 13:48:00] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.61624/nu1.mnc ./tmp.mri_nu_correct.mni.61624/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.61624/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.61624/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.61624/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.61624/ones.mgz sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi input ./tmp.mri_nu_correct.mni.61624/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.61624/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.61624/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.61624/sum.junk --avgwf ./tmp.mri_nu_correct.mni.61624/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.61624/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.61624/sum.junk --avgwf ./tmp.mri_nu_correct.mni.61624/input.mean.dat sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 Loading ./tmp.mri_nu_correct.mni.61624/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.61624/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.61624/ones.mgz --i ./tmp.mri_nu_correct.mni.61624/nu2.mnc --sum ./tmp.mri_nu_correct.mni.61624/sum.junk --avgwf ./tmp.mri_nu_correct.mni.61624/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.61624/ones.mgz --i ./tmp.mri_nu_correct.mni.61624/nu2.mnc --sum ./tmp.mri_nu_correct.mni.61624/sum.junk --avgwf ./tmp.mri_nu_correct.mni.61624/output.mean.dat sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 Loading ./tmp.mri_nu_correct.mni.61624/ones.mgz Loading ./tmp.mri_nu_correct.mni.61624/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.61624/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.61624/nu2.mnc ./tmp.mri_nu_correct.mni.61624/nu2.mnc mul 1.06007866491596147825 Saving result to './tmp.mri_nu_correct.mni.61624/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.61624/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.61624/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.61624/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-08, -8.3819e-08) j_ras = (6.14673e-08, -5.52391e-08, -1) k_ras = (2.2538e-07, 1, 1.83936e-08) 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 6 seconds. mapping ( 2, 129) to ( 3, 110) Mon Oct 13 13:48:46 CEST 2014 mri_nu_correct.mni done mri_add_xform_to_header -c /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Oct 13 13:48:47 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.032 -0.033 -0.044 -3.473; 0.066 0.826 0.510 -23.435; 0.004 -0.463 0.955 -10.961; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 53 (52), valley at 35 (34) csf peak at 12, setting threshold to 39 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 51 (50), valley at 25 (24) csf peak at 13, setting threshold to 38 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 54 seconds. #-------------------------------------------- #@# Skull Stripping Mon Oct 13 13:50:41 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=11.0 skull bounding box = (44, 45, 15) --> (207, 255, 255) using (98, 115, 135) as brain centroid... mean wm in atlas = 126, using box (78,89,105) --> (118, 140,164) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 104, scaling input intensities by 1.212 scaling channel 0 by 1.21154 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.610849 @ (-9.091, -9.091, -27.273) max log p = -4.529203 @ (4.545, -4.545, 4.545) max log p = -4.470553 @ (2.273, 2.273, 6.818) max log p = -4.470553 @ (0.000, 0.000, 0.000) max log p = -4.450738 @ (0.568, -0.568, -0.568) max log p = -4.450738 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -11.9, -16.5): log p = -4.451 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.5 (thresh=-4.4) 1.064 0.000 0.000 -9.830; 0.000 0.996 0.575 -74.335; 0.000 -0.532 0.921 70.310; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.064 0.000 0.000 -9.830; 0.000 0.996 0.575 -74.335; 0.000 -0.492 0.852 72.989; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.064 0.000 0.000 -9.830; 0.000 0.996 0.575 -74.335; 0.000 -0.492 0.852 72.989; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.043 -0.048 0.012 -2.234; 0.034 1.043 0.528 -79.532; -0.032 -0.410 0.854 64.242; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.063 -0.015 0.031 -11.294; -0.001 1.011 0.545 -74.665; -0.033 -0.444 0.837 70.829; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.058 -0.030 0.040 -10.214; 0.007 1.011 0.554 -75.341; -0.051 -0.452 0.833 75.037; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-3.9) 1.058 -0.030 0.040 -10.214; 0.007 1.011 0.554 -75.341; -0.051 -0.452 0.833 75.037; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05823 -0.03049 0.04020 -10.21404; 0.00744 1.01100 0.55352 -75.34107; -0.05085 -0.45230 0.83350 75.03712; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05823 -0.03049 0.04020 -10.21404; 0.00744 1.01100 0.55352 -75.34107; -0.05085 -0.45230 0.83350 75.03712; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.058 -0.030 0.040 -10.214; 0.007 1.011 0.554 -75.341; -0.051 -0.452 0.833 75.037; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.8) transform before final EM align: 1.058 -0.030 0.040 -10.214; 0.007 1.011 0.554 -75.341; -0.051 -0.452 0.833 75.037; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05823 -0.03049 0.04020 -10.21404; 0.00744 1.01100 0.55352 -75.34107; -0.05085 -0.45230 0.83350 75.03712; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05823 -0.03049 0.04020 -10.21404; 0.00744 1.01100 0.55352 -75.34107; -0.05085 -0.45230 0.83350 75.03712; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.3 tol 0.000000 final transform: 1.058 -0.030 0.040 -10.214; 0.007 1.011 0.554 -75.341; -0.051 -0.452 0.833 75.037; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 26 minutes and 3 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.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=120 r=86 first estimation of the main basin volume: 2723132 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=109, y=115, z=79, Imax=255 CSF=17, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=13111364734 voxels, voxel volume =1.000 = 13111364734 mmm3 = 13111364.608 cm3 done. PostAnalyze...Basin Prior 10 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=145,y=145, z=128, r=124108 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=15, CSF_MAX=36 , nb = 45026 RIGHT_CER CSF_MIN=0, CSF_intensity=19, CSF_MAX=47 , nb = -1034378565 LEFT_CER CSF_MIN=0, CSF_intensity=7, CSF_MAX=63 , nb = 1085184231 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=12, CSF_MAX=29 , nb = -1051980147 LEFT_BRAIN CSF_MIN=0, CSF_intensity=15, CSF_MAX=35 , nb = 1073931514 OTHER CSF_MIN=1, CSF_intensity=9, CSF_MAX=22 , nb = 1074067626 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 36, 29, 24, 43 after analyzing : 25, 29, 29, 32 RIGHT_CER before analyzing : 47, 37, 25, 60 after analyzing : 32, 37, 37, 42 LEFT_CER before analyzing : 63, 38, 24, 58 after analyzing : 30, 38, 38, 43 RIGHT_BRAIN before analyzing : 29, 26, 23, 43 after analyzing : 22, 26, 26, 30 LEFT_BRAIN before analyzing : 35, 29, 24, 43 after analyzing : 25, 29, 29, 32 OTHER before analyzing : 22, 39, 70, 93 after analyzing : 22, 59, 70, 67 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...103 iterations *********************VALIDATION********************* curvature mean = -0.009, std = 0.022 curvature mean = 69.579, std = 12.477 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 13.72, sigma = 38.49 after rotation: sse = 13.72, sigma = 38.49 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 19.28, its var is 35.45 before Erosion-Dilatation 19.40% of inacurate vertices after Erosion-Dilatation 28.80% of inacurate vertices 51.83% of 'positive' inacurate vertices 48.17% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...41 iterations mri_strip_skull: done peeling brain Brain Size = 1833202 voxels, voxel volume = 1.000 mm3 = 1833202 mmm3 = 1833.202 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Mon Oct 13 14:17:10 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (62, 63, 36) --> (196, 201, 186) using (107, 109, 111) as brain centroid... mean wm in atlas = 107, using box (91,92,93) --> (123, 125,129) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.294333 @ (-9.091, -9.091, -9.091) max log p = -4.230141 @ (4.545, -4.545, -4.545) max log p = -4.164352 @ (2.273, 2.273, 2.273) max log p = -4.164352 @ (0.000, 0.000, 0.000) max log p = -4.153849 @ (-0.568, 2.841, 1.705) max log p = -4.153849 @ (0.000, 0.000, 0.000) Found translation: (-2.8, -8.5, -9.7): log p = -4.154 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-4.2 (thresh=-4.1) 1.064 0.000 0.000 -11.106; 0.000 0.996 0.575 -74.121; 0.000 -0.457 0.791 72.534; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.7, old_max_log_p =-3.7 (thresh=-3.7) 1.064 0.000 0.000 -11.106; 0.000 0.996 0.575 -74.121; 0.000 -0.457 0.791 72.534; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.7 (thresh=-3.7) 1.041 -0.061 0.032 -4.066; 0.035 0.994 0.576 -78.590; -0.072 -0.473 0.819 84.486; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.024 -0.013 0.024 -7.145; 0.001 0.977 0.565 -70.607; -0.039 -0.484 0.835 79.744; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.021 -0.061 0.033 -1.639; 0.034 0.975 0.566 -74.913; -0.074 -0.492 0.850 83.743; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.021 -0.061 0.033 -1.639; 0.034 0.975 0.566 -74.913; -0.074 -0.492 0.850 83.743; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.020 -0.061 0.033 -1.488; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.847 83.351; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02264 -0.06079 0.03271 -1.78854; 0.03414 0.97869 0.56846 -76.06355; -0.07328 -0.48972 0.84567 83.37627; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.02264 -0.06079 0.03271 -1.78854; 0.03414 0.97869 0.56846 -76.06355; -0.07328 -0.48972 0.84567 83.37627; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.6 (old=-4.4) transform before final EM align: 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.02264 -0.06079 0.03271 -1.78854; 0.03414 0.97869 0.56846 -76.06355; -0.07328 -0.48972 0.84567 83.37627; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.02264 -0.06079 0.03271 -1.78854; 0.03414 0.97869 0.56846 -76.06355; -0.07328 -0.48972 0.84567 83.37627; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 013: -log(p) = 4.0 tol 0.000000 final transform: 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 26 minutes and 29 seconds. #-------------------------------------- #@# CA Normalize Mon Oct 13 14:43:39 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.0 skull bounding box = (62, 63, 36) --> (196, 201, 186) using (107, 109, 111) as brain centroid... mean wm in atlas = 107, using box (91,92,93) --> (123, 125,129) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 65, 41) --> (195, 189, 198) Left_Cerebral_White_Matter: limiting intensities to 89.0 --> 189.0 1 of 970 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 66, 43) --> (130, 185, 198) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 189.0 0 of 705 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 157, 81) --> (181, 197, 131) Left_Cerebellum_White_Matter: limiting intensities to 105.0 --> 189.0 9 of 11 (81.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 157, 75) --> (133, 200, 130) Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 189.0 0 of 17 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 139, 105) --> (146, 200, 138) Brain_Stem: limiting intensities to 100.0 --> 189.0 0 of 13 (0.0%) samples deleted using 1716 total control points for intensity normalization... bias field = 1.045 +- 0.052 11 of 1706 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 65, 41) --> (195, 189, 198) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 196.0 6 of 966 (0.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 66, 43) --> (130, 185, 198) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 196.0 0 of 752 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 157, 81) --> (181, 197, 131) Left_Cerebellum_White_Matter: limiting intensities to 89.0 --> 196.0 0 of 57 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 157, 75) --> (133, 200, 130) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 196.0 0 of 67 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 139, 105) --> (146, 200, 138) Brain_Stem: limiting intensities to 102.0 --> 196.0 46 of 68 (67.6%) samples deleted using 1910 total control points for intensity normalization... bias field = 0.996 +- 0.050 1 of 1858 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 65, 41) --> (195, 189, 198) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 194.0 1 of 1068 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (65, 66, 43) --> (130, 185, 198) Right_Cerebral_White_Matter: limiting intensities to 87.0 --> 194.0 1 of 902 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (133, 157, 81) --> (181, 197, 131) Left_Cerebellum_White_Matter: limiting intensities to 86.0 --> 194.0 0 of 88 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 157, 75) --> (133, 200, 130) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 194.0 0 of 57 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 139, 105) --> (146, 200, 138) Brain_Stem: limiting intensities to 86.0 --> 194.0 29 of 169 (17.2%) samples deleted using 2284 total control points for intensity normalization... bias field = 0.998 +- 0.046 2 of 2253 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 29 seconds. #-------------------------------------- #@# CA Reg Mon Oct 13 14:45:08 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.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... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.14 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.978, neg=0, invalid=96777 0001: dt=129.472000, rms=0.929 (5.029%), neg=0, invalid=96777 0002: dt=443.904000, rms=0.888 (4.343%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.875 (1.467%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.872 (0.381%), neg=0, invalid=96777 0005: dt=369.920000, rms=0.862 (1.187%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.858 (0.383%), neg=0, invalid=96777 0007: dt=32.368000, rms=0.857 (0.128%), neg=0, invalid=96777 0008: dt=32.368000, rms=0.857 (0.051%), neg=0, invalid=96777 0009: dt=32.368000, rms=0.856 (0.047%), neg=0, invalid=96777 0010: dt=32.368000, rms=0.856 (0.100%), neg=0, invalid=96777 0011: dt=32.368000, rms=0.854 (0.225%), neg=0, invalid=96777 0012: dt=32.368000, rms=0.851 (0.353%), neg=0, invalid=96777 0013: dt=32.368000, rms=0.847 (0.419%), neg=0, invalid=96777 0014: dt=32.368000, rms=0.844 (0.407%), neg=0, invalid=96777 0015: dt=32.368000, rms=0.841 (0.366%), neg=0, invalid=96777 0016: dt=32.368000, rms=0.838 (0.343%), neg=0, invalid=96777 0017: dt=32.368000, rms=0.835 (0.317%), neg=0, invalid=96777 0018: dt=32.368000, rms=0.833 (0.281%), neg=0, invalid=96777 0019: dt=32.368000, rms=0.830 (0.273%), neg=0, invalid=96777 0020: dt=32.368000, rms=0.828 (0.302%), neg=0, invalid=96777 0021: dt=32.368000, rms=0.825 (0.346%), neg=0, invalid=96777 0022: dt=32.368000, rms=0.822 (0.352%), neg=0, invalid=96777 0023: dt=32.368000, rms=0.820 (0.319%), neg=0, invalid=96777 0024: dt=32.368000, rms=0.817 (0.285%), neg=0, invalid=96777 0025: dt=32.368000, rms=0.815 (0.252%), neg=0, invalid=96777 0026: dt=32.368000, rms=0.813 (0.220%), neg=0, invalid=96777 0027: dt=32.368000, rms=0.812 (0.195%), neg=0, invalid=96777 0028: dt=32.368000, rms=0.810 (0.198%), neg=0, invalid=96777 0029: dt=32.368000, rms=0.808 (0.210%), neg=0, invalid=96777 0030: dt=32.368000, rms=0.807 (0.223%), neg=0, invalid=96777 0031: dt=32.368000, rms=0.805 (0.223%), neg=0, invalid=96777 0032: dt=32.368000, rms=0.803 (0.216%), neg=0, invalid=96777 0033: dt=32.368000, rms=0.801 (0.197%), neg=0, invalid=96777 0034: dt=32.368000, rms=0.800 (0.173%), neg=0, invalid=96777 0035: dt=32.368000, rms=0.799 (0.149%), neg=0, invalid=96777 0036: dt=32.368000, rms=0.798 (0.131%), neg=0, invalid=96777 0037: dt=32.368000, rms=0.797 (0.131%), neg=0, invalid=96777 0038: dt=32.368000, rms=0.796 (0.141%), neg=0, invalid=96777 0039: dt=32.368000, rms=0.794 (0.155%), neg=0, invalid=96777 0040: dt=32.368000, rms=0.793 (0.162%), neg=0, invalid=96777 0041: dt=32.368000, rms=0.792 (0.153%), neg=0, invalid=96777 0042: dt=32.368000, rms=0.791 (0.141%), neg=0, invalid=96777 0043: dt=32.368000, rms=0.790 (0.123%), neg=0, invalid=96777 0044: dt=32.368000, rms=0.789 (0.106%), neg=0, invalid=96777 0045: dt=517.888000, rms=0.789 (0.053%), neg=0, invalid=96777 0046: dt=517.888000, rms=0.787 (0.184%), neg=0, invalid=96777 0047: dt=517.888000, rms=0.787 (-6.845%), neg=0, invalid=96777 0048: dt=32.368000, rms=0.786 (0.134%), neg=0, invalid=96777 0049: dt=27.744000, rms=0.786 (0.031%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.786, neg=0, invalid=96777 0050: dt=32.368000, rms=0.786 (0.049%), neg=0, invalid=96777 0051: dt=73.984000, rms=0.785 (0.042%), neg=0, invalid=96777 0052: dt=73.984000, rms=0.785 (0.064%), neg=0, invalid=96777 0053: dt=73.984000, rms=0.784 (0.062%), neg=0, invalid=96777 0054: dt=73.984000, rms=0.784 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.791, neg=0, invalid=96777 0055: dt=145.152000, rms=0.770 (2.643%), neg=0, invalid=96777 0056: dt=82.944000, rms=0.760 (1.289%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.750 (1.361%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.748 (0.228%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.744 (0.531%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.739 (0.719%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.733 (0.832%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.726 (0.956%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.718 (1.058%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.711 (0.968%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.706 (0.756%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.701 (0.618%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.697 (0.578%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.694 (0.520%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.691 (0.434%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.688 (0.352%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.686 (0.291%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.685 (0.264%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.683 (0.225%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.682 (0.157%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.681 (0.131%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.680 (0.135%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.679 (0.172%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.678 (0.175%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.677 (0.155%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.676 (0.153%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.674 (0.178%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.673 (0.179%), neg=0, invalid=96777 0083: dt=36.288000, rms=0.672 (0.169%), neg=0, invalid=96777 0084: dt=36.288000, rms=0.671 (0.164%), neg=0, invalid=96777 0085: dt=36.288000, rms=0.670 (0.140%), neg=0, invalid=96777 0086: dt=36.288000, rms=0.669 (0.132%), neg=0, invalid=96777 0087: dt=36.288000, rms=0.668 (0.135%), neg=0, invalid=96777 0088: dt=36.288000, rms=0.667 (0.129%), neg=0, invalid=96777 0089: dt=36.288000, rms=0.667 (0.104%), neg=0, invalid=96777 0090: dt=36.288000, rms=0.666 (0.092%), neg=0, invalid=96777 0091: dt=124.416000, rms=0.666 (0.091%), neg=0, invalid=96777 0092: dt=124.416000, rms=0.666 (-0.727%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.666, neg=0, invalid=96777 0093: dt=20.736000, rms=0.665 (0.048%), neg=0, invalid=96777 0094: dt=36.288000, rms=0.665 (0.043%), neg=0, invalid=96777 0095: dt=36.288000, rms=0.665 (0.022%), neg=0, invalid=96777 0096: dt=36.288000, rms=0.665 (-0.024%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0097: dt=0.175000, rms=0.703 (0.000%), neg=0, invalid=96777 0098: dt=0.037500, rms=0.703 (0.001%), neg=0, invalid=96777 0099: dt=0.007811, rms=0.703 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0100: dt=0.000000, rms=0.703 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.815, neg=0, invalid=96777 0101: dt=4.743692, rms=0.783 (3.944%), neg=0, invalid=96777 0102: dt=3.456000, rms=0.780 (0.381%), neg=0, invalid=96777 0103: dt=1.008000, rms=0.780 (0.020%), neg=0, invalid=96777 0104: dt=1.008000, rms=0.780 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.780, neg=0, invalid=96777 0105: dt=0.000000, rms=0.780 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.868, neg=0, invalid=96777 0106: dt=0.857143, rms=0.865 (0.385%), neg=0, invalid=96777 0107: dt=1.606695, rms=0.860 (0.542%), neg=0, invalid=96777 0108: dt=1.296296, rms=0.859 (0.171%), neg=0, invalid=96777 0109: dt=1.296296, rms=0.858 (0.057%), neg=0, invalid=96777 0110: dt=1.296296, rms=0.858 (-0.203%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.858, neg=0, invalid=96777 0111: dt=0.527778, rms=0.858 (0.069%), neg=0, invalid=96777 0112: dt=0.000000, rms=0.858 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.794, neg=0, invalid=96777 0113: dt=0.320000, rms=0.776 (2.282%), neg=0, invalid=96777 0114: dt=0.000000, rms=0.776 (0.005%), neg=0, invalid=96777 0115: dt=0.050000, rms=0.776 (-0.245%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.776, neg=0, invalid=96777 0116: dt=0.000000, rms=0.776 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.36113 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (2712 voxels, overlap=0.003) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2712 voxels, peak = 5), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.31165 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (2306 voxels, overlap=0.004) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (2306 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.07598 (114) Right_Pallidum (52): linear fit = 1.14 x + 0.0 (522 voxels, overlap=0.281) Right_Pallidum (52): linear fit = 1.14 x + 0.0 (522 voxels, peak = 114), gca=114.5 gca peak = 0.19192 (97) mri peak = 0.10582 (107) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (467 voxels, overlap=0.728) Left_Pallidum (13): linear fit = 1.10 x + 0.0 (467 voxels, peak = 106), gca=106.2 gca peak = 0.24007 (63) mri peak = 0.07935 (51) Right_Hippocampus (53): linear fit = 0.80 x + 0.0 (811 voxels, overlap=0.019) Right_Hippocampus (53): linear fit = 0.80 x + 0.0 (811 voxels, peak = 50), gca=50.1 gca peak = 0.29892 (64) mri peak = 0.07369 (51) Left_Hippocampus (17): linear fit = 0.76 x + 0.0 (568 voxels, overlap=0.012) Left_Hippocampus (17): linear fit = 0.76 x + 0.0 (568 voxels, peak = 49), gca=49.0 gca peak = 0.12541 (104) mri peak = 0.07582 (111) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68488 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68488 voxels, peak = 110), gca=109.7 gca peak = 0.13686 (104) mri peak = 0.07518 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (78234 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (78234 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.04610 (42) Left_Cerebral_Cortex (3): linear fit = 0.69 x + 0.0 (28632 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 0.69 x + 0.0 (28632 voxels, peak = 43), gca=43.2 gca peak = 0.13270 (63) mri peak = 0.03861 (42) Right_Cerebral_Cortex (42): linear fit = 0.69 x + 0.0 (27293 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 0.69 x + 0.0 (27293 voxels, peak = 44), gca=43.8 gca peak = 0.15182 (70) mri peak = 0.15000 (60) Right_Caudate (50): linear fit = 0.81 x + 0.0 (488 voxels, overlap=0.079) Right_Caudate (50): linear fit = 0.81 x + 0.0 (488 voxels, peak = 56), gca=56.4 gca peak = 0.14251 (76) mri peak = 0.09304 (74) Left_Caudate (11): linear fit = 0.93 x + 0.0 (764 voxels, overlap=0.513) Left_Caudate (11): linear fit = 0.93 x + 0.0 (764 voxels, peak = 70), gca=70.3 gca peak = 0.12116 (60) mri peak = 0.03435 (46) Left_Cerebellum_Cortex (8): linear fit = 0.75 x + 0.0 (29132 voxels, overlap=0.023) Left_Cerebellum_Cortex (8): linear fit = 0.75 x + 0.0 (29132 voxels, peak = 45), gca=44.7 gca peak = 0.12723 (61) mri peak = 0.03520 (44) Right_Cerebellum_Cortex (47): linear fit = 0.76 x + 0.0 (28488 voxels, overlap=0.012) Right_Cerebellum_Cortex (47): linear fit = 0.76 x + 0.0 (28488 voxels, peak = 47), gca=46.7 gca peak = 0.22684 (88) mri peak = 0.06867 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8293 voxels, overlap=0.131) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (8293 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.06150 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6816 voxels, overlap=0.379) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6816 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.11471 (56) Left_Amygdala (18): linear fit = 0.83 x + 0.0 (413 voxels, overlap=0.404) Left_Amygdala (18): linear fit = 0.83 x + 0.0 (413 voxels, peak = 52), gca=51.8 gca peak = 0.39668 (62) mri peak = 0.14126 (53) Right_Amygdala (54): linear fit = 0.85 x + 0.0 (366 voxels, overlap=0.037) Right_Amygdala (54): linear fit = 0.85 x + 0.0 (366 voxels, peak = 52), gca=52.4 gca peak = 0.10129 (93) mri peak = 0.05199 (100) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5742 voxels, overlap=0.828) Left_Thalamus_Proper (10): linear fit = 1.04 x + 0.0 (5742 voxels, peak = 97), gca=97.2 gca peak = 0.12071 (89) mri peak = 0.04897 (80) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3347 voxels, overlap=0.961) Right_Thalamus_Proper (49): linear fit = 1.04 x + 0.0 (3347 voxels, peak = 93), gca=93.0 gca peak = 0.13716 (82) mri peak = 0.05320 (78) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2961 voxels, overlap=0.985) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2961 voxels, peak = 80), gca=80.0 gca peak = 0.15214 (84) mri peak = 0.03872 (107) Right_Putamen (51): linear fit = 1.22 x + 0.0 (2682 voxels, overlap=0.172) Right_Putamen (51): linear fit = 1.22 x + 0.0 (2682 voxels, peak = 102), gca=102.1 gca peak = 0.08983 (85) mri peak = 0.05553 (99) Brain_Stem (16): linear fit = 1.15 x + 0.0 (12010 voxels, overlap=0.543) Brain_Stem (16): linear fit = 1.15 x + 0.0 (12010 voxels, peak = 98), gca=98.2 gca peak = 0.11809 (92) mri peak = 0.10365 (106) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (893 voxels, overlap=0.189) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (893 voxels, peak = 104), gca=103.5 gca peak = 0.12914 (94) mri peak = 0.10132 (105) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1262 voxels, overlap=0.113) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1262 voxels, peak = 106), gca=105.8 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.20534 (10) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (421 voxels, overlap=0.015) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (421 voxels, peak = 9), gca=8.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.77 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 Left_Pallidum too bright - rescaling by 0.997 (from 1.095) to 105.9 (was 106.2) Right_Putamen too bright - rescaling by 0.963 (from 1.215) to 98.3 (was 102.1) Right_Pallidum too bright - rescaling by 0.925 (from 1.145) to 105.9 (was 114.5) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.814, neg=0, invalid=96777 0117: dt=32.368000, rms=0.808 (0.725%), neg=0, invalid=96777 0118: dt=5.780000, rms=0.808 (0.090%), neg=0, invalid=96777 0119: dt=0.433500, rms=0.808 (0.007%), neg=0, invalid=96777 0120: dt=0.003387, rms=0.808 (0.000%), neg=0, invalid=96777 0121: dt=0.001693, rms=0.808 (0.000%), neg=0, invalid=96777 0122: dt=0.000423, rms=0.808 (0.000%), neg=0, invalid=96777 0123: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0124: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0125: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0126: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0127: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0128: dt=0.000000, rms=0.808 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0129: dt=4.032000, rms=0.751 (7.009%), neg=0, invalid=96777 0130: dt=4.032000, rms=0.715 (4.811%), neg=0, invalid=96777 0131: dt=4.032000, rms=0.691 (3.412%), neg=0, invalid=96777 0132: dt=4.032000, rms=0.673 (2.513%), neg=0, invalid=96777 0133: dt=4.032000, rms=0.661 (1.880%), neg=0, invalid=96777 0134: dt=4.032000, rms=0.651 (1.445%), neg=0, invalid=96777 0135: dt=4.032000, rms=0.644 (1.128%), neg=0, invalid=96777 0136: dt=11.520000, rms=0.627 (2.518%), neg=0, invalid=96777 0137: dt=4.032000, rms=0.625 (0.424%), neg=0, invalid=96777 0138: dt=16.128000, rms=0.616 (1.448%), neg=0, invalid=96777 0139: dt=4.032000, rms=0.615 (0.155%), neg=0, invalid=96777 0140: dt=4.032000, rms=0.614 (0.194%), neg=0, invalid=96777 0141: dt=4.032000, rms=0.613 (0.154%), neg=0, invalid=96777 0142: dt=4.032000, rms=0.612 (0.155%), neg=0, invalid=96777 0143: dt=4.032000, rms=0.611 (0.124%), neg=0, invalid=96777 0144: dt=11.520000, rms=0.609 (0.337%), neg=0, invalid=96777 0145: dt=4.869565, rms=0.608 (0.105%), neg=0, invalid=96777 0146: dt=4.555556, rms=0.607 (0.120%), neg=0, invalid=96777 0147: dt=4.032000, rms=0.607 (0.072%), neg=0, invalid=96777 0148: dt=5.217391, rms=0.606 (0.120%), neg=0, invalid=96777 0149: dt=4.032000, rms=0.606 (0.050%), neg=0, invalid=96777 0150: dt=4.032000, rms=0.605 (0.103%), neg=0, invalid=96777 0151: dt=4.032000, rms=0.605 (0.059%), neg=0, invalid=96777 0152: dt=4.032000, rms=0.604 (0.117%), neg=0, invalid=96777 0153: dt=4.032000, rms=0.603 (0.181%), neg=0, invalid=96777 0154: dt=4.032000, rms=0.602 (0.193%), neg=0, invalid=96777 0155: dt=4.032000, rms=0.601 (0.215%), neg=0, invalid=96777 0156: dt=4.032000, rms=0.600 (0.211%), neg=0, invalid=96777 0157: dt=4.032000, rms=0.598 (0.240%), neg=0, invalid=96777 0158: dt=4.032000, rms=0.597 (0.204%), neg=0, invalid=96777 0159: dt=4.032000, rms=0.596 (0.169%), neg=0, invalid=96777 0160: dt=4.032000, rms=0.595 (0.142%), neg=0, invalid=96777 0161: dt=4.032000, rms=0.594 (0.172%), neg=0, invalid=96777 0162: dt=4.032000, rms=0.593 (0.110%), neg=0, invalid=96777 0163: dt=4.032000, rms=0.593 (0.084%), neg=0, invalid=96777 0164: dt=4.032000, rms=0.592 (0.076%), neg=0, invalid=96777 0165: dt=4.032000, rms=0.592 (0.101%), neg=0, invalid=96777 0166: dt=4.032000, rms=0.591 (0.080%), neg=0, invalid=96777 0167: dt=4.032000, rms=0.591 (0.058%), neg=0, invalid=96777 0168: dt=4.032000, rms=0.591 (0.039%), neg=0, invalid=96777 0169: dt=4.032000, rms=0.590 (0.045%), neg=0, invalid=96777 0170: dt=4.032000, rms=0.590 (0.043%), neg=0, invalid=96777 0171: dt=4.032000, rms=0.590 (0.040%), neg=0, invalid=96777 0172: dt=4.032000, rms=0.590 (0.043%), neg=0, invalid=96777 0173: dt=4.032000, rms=0.590 (0.040%), neg=0, invalid=96777 0174: dt=4.032000, rms=0.589 (0.036%), neg=0, invalid=96777 0175: dt=4.032000, rms=0.589 (0.031%), neg=0, invalid=96777 0176: dt=4.032000, rms=0.589 (0.030%), neg=0, invalid=96777 0177: dt=4.032000, rms=0.589 (0.032%), neg=0, invalid=96777 0178: dt=4.032000, rms=0.589 (0.024%), neg=0, invalid=96777 0179: dt=4.032000, rms=0.588 (0.020%), neg=0, invalid=96777 0180: dt=4.032000, rms=0.588 (0.009%), neg=0, invalid=96777 0181: dt=4.032000, rms=0.588 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.588, neg=0, invalid=96777 0182: dt=0.000000, rms=0.588 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=96777 0183: dt=0.000000, rms=0.613 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=96777 0184: dt=0.000000, rms=0.613 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.572, neg=0, invalid=96777 0185: dt=0.177481, rms=0.563 (1.548%), neg=0, invalid=96777 0186: dt=0.145833, rms=0.558 (0.851%), neg=0, invalid=96777 0187: dt=0.028000, rms=0.557 (0.122%), neg=0, invalid=96777 0188: dt=0.080000, rms=0.555 (0.337%), neg=0, invalid=96777 0189: dt=0.005000, rms=0.555 (0.019%), neg=0, invalid=96777 0190: dt=0.005000, rms=0.555 (0.019%), neg=0, invalid=96777 0191: dt=0.005000, rms=0.555 (0.033%), neg=0, invalid=96777 0192: dt=0.005000, rms=0.555 (0.048%), neg=0, invalid=96777 0193: dt=0.005000, rms=0.554 (0.061%), neg=0, invalid=96777 0194: dt=0.005000, rms=0.554 (0.072%), neg=0, invalid=96777 0195: dt=0.005000, rms=0.554 (0.082%), neg=0, invalid=96777 0196: dt=0.005000, rms=0.553 (0.090%), neg=0, invalid=96777 0197: dt=0.005000, rms=0.553 (0.095%), neg=0, invalid=96777 0198: dt=0.005000, rms=0.552 (0.099%), neg=0, invalid=96777 0199: dt=0.005000, rms=0.551 (0.104%), neg=0, invalid=96777 0200: dt=0.005000, rms=0.551 (0.106%), neg=0, invalid=96777 0201: dt=0.005000, rms=0.550 (0.106%), neg=0, invalid=96777 0202: dt=0.005000, rms=0.550 (0.107%), neg=0, invalid=96777 0203: dt=0.005000, rms=0.549 (0.110%), neg=0, invalid=96777 0204: dt=0.005000, rms=0.549 (0.105%), neg=0, invalid=96777 0205: dt=0.005000, rms=0.548 (0.103%), neg=0, invalid=96777 0206: dt=0.005000, rms=0.547 (0.098%), neg=0, invalid=96777 0207: dt=0.005000, rms=0.547 (0.100%), neg=0, invalid=96777 0208: dt=0.005000, rms=0.546 (0.092%), neg=0, invalid=96777 0209: dt=0.005000, rms=0.546 (0.092%), neg=0, invalid=96777 0210: dt=0.005000, rms=0.545 (0.087%), neg=0, invalid=96777 0211: dt=0.005000, rms=0.545 (0.083%), neg=0, invalid=96777 0212: dt=0.002500, rms=0.545 (0.001%), neg=0, invalid=96777 0213: dt=0.002500, rms=0.545 (0.005%), neg=0, invalid=96777 0214: dt=0.002500, rms=0.545 (0.006%), neg=0, invalid=96777 0215: dt=0.002500, rms=0.545 (0.008%), neg=0, invalid=96777 0216: dt=0.002500, rms=0.545 (0.008%), neg=0, invalid=96777 0217: dt=0.028000, rms=0.545 (0.026%), neg=0, invalid=96777 0218: dt=0.007000, rms=0.545 (0.006%), neg=0, invalid=96777 0219: dt=0.007000, rms=0.545 (0.005%), neg=0, invalid=96777 0220: dt=0.007000, rms=0.545 (0.014%), neg=0, invalid=96777 0221: dt=0.007000, rms=0.544 (0.017%), neg=0, invalid=96777 0222: dt=0.007000, rms=0.544 (0.022%), neg=0, invalid=96777 0223: dt=0.007000, rms=0.544 (0.024%), neg=0, invalid=96777 0224: dt=0.007000, rms=0.544 (0.025%), neg=0, invalid=96777 0225: dt=0.007000, rms=0.544 (0.034%), neg=0, invalid=96777 0226: dt=0.007000, rms=0.544 (0.035%), neg=0, invalid=96777 0227: dt=0.007000, rms=0.543 (0.035%), neg=0, invalid=96777 0228: dt=0.007000, rms=0.543 (0.037%), neg=0, invalid=96777 0229: dt=0.007000, rms=0.543 (0.033%), neg=0, invalid=96777 0230: dt=0.007000, rms=0.543 (0.037%), neg=0, invalid=96777 0231: dt=0.007000, rms=0.543 (0.037%), neg=0, invalid=96777 0232: dt=0.007000, rms=0.542 (0.038%), neg=0, invalid=96777 0233: dt=0.007000, rms=0.542 (0.006%), neg=0, invalid=96777 0234: dt=0.007000, rms=0.542 (0.008%), neg=0, invalid=96777 0235: dt=0.007000, rms=0.542 (0.012%), neg=0, invalid=96777 0236: dt=0.007000, rms=0.542 (0.013%), neg=0, invalid=96777 0237: dt=0.007000, rms=0.542 (0.020%), neg=0, invalid=96777 0238: dt=0.007000, rms=0.542 (0.022%), neg=0, invalid=96777 0239: dt=0.007000, rms=0.542 (0.017%), neg=0, invalid=96777 0240: dt=0.112000, rms=0.542 (0.065%), neg=0, invalid=96777 0241: dt=0.096000, rms=0.541 (0.044%), neg=0, invalid=96777 0242: dt=0.000750, rms=0.541 (-0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.541, neg=0, invalid=96777 0243: dt=0.001250, rms=0.541 (0.003%), neg=0, invalid=96777 0244: dt=0.001750, rms=0.541 (0.004%), neg=0, invalid=96777 0245: dt=0.007000, rms=0.541 (0.015%), neg=0, invalid=96777 0246: dt=0.006000, rms=0.541 (0.016%), neg=0, invalid=96777 0247: dt=0.007000, rms=0.541 (0.016%), neg=0, invalid=96777 0248: dt=0.007000, rms=0.541 (0.013%), neg=0, invalid=96777 0249: dt=0.007000, rms=0.541 (0.025%), neg=0, invalid=96777 0250: dt=0.007000, rms=0.541 (0.041%), neg=0, invalid=96777 0251: dt=0.007000, rms=0.540 (0.050%), neg=0, invalid=96777 0252: dt=0.007000, rms=0.540 (0.055%), neg=0, invalid=96777 0253: dt=0.007000, rms=0.540 (0.059%), neg=0, invalid=96777 0254: dt=0.007000, rms=0.539 (0.063%), neg=0, invalid=96777 0255: dt=0.003500, rms=0.539 (0.004%), neg=0, invalid=96777 0256: dt=0.003500, rms=0.539 (0.007%), neg=0, invalid=96777 0257: dt=0.003500, rms=0.539 (0.012%), neg=0, invalid=96777 0258: dt=0.003500, rms=0.539 (0.010%), neg=0, invalid=96777 0259: dt=0.112000, rms=0.538 (0.158%), neg=0, invalid=96777 0260: dt=0.007000, rms=0.538 (0.005%), neg=0, invalid=96777 0261: dt=0.007000, rms=0.538 (0.007%), neg=0, invalid=96777 0262: dt=0.007000, rms=0.538 (0.014%), neg=0, invalid=96777 0263: dt=0.007000, rms=0.538 (0.019%), neg=0, invalid=96777 0264: dt=0.007000, rms=0.538 (0.026%), neg=0, invalid=96777 0265: dt=0.007000, rms=0.538 (0.032%), neg=0, invalid=96777 0266: dt=0.007000, rms=0.538 (0.031%), neg=0, invalid=96777 0267: dt=0.007000, rms=0.538 (0.032%), neg=0, invalid=96777 0268: dt=0.003500, rms=0.538 (0.005%), neg=0, invalid=96777 0269: dt=0.003500, rms=0.538 (0.004%), neg=0, invalid=96777 0270: dt=0.007000, rms=0.537 (0.005%), neg=0, invalid=96777 0271: dt=0.007000, rms=0.537 (0.006%), neg=0, invalid=96777 0272: dt=0.024000, rms=0.537 (0.017%), neg=0, invalid=96777 0273: dt=0.007000, rms=0.537 (0.008%), neg=0, invalid=96777 0274: dt=0.007000, rms=0.537 (0.005%), neg=0, invalid=96777 0275: dt=0.007000, rms=0.537 (0.009%), neg=0, invalid=96777 0276: dt=0.007000, rms=0.537 (0.014%), neg=0, invalid=96777 0277: dt=0.007000, rms=0.537 (0.018%), neg=0, invalid=96777 0278: dt=0.007000, rms=0.537 (0.018%), neg=0, invalid=96777 0279: dt=0.007000, rms=0.537 (0.022%), neg=0, invalid=96777 0280: dt=0.007000, rms=0.537 (0.027%), neg=0, invalid=96777 0281: dt=0.007000, rms=0.537 (0.025%), neg=0, invalid=96777 0282: dt=0.007000, rms=0.536 (0.027%), neg=0, invalid=96777 0283: dt=0.007000, rms=0.536 (0.027%), neg=0, invalid=96777 0284: dt=0.007000, rms=0.536 (0.027%), neg=0, invalid=96777 0285: dt=0.007000, rms=0.536 (0.027%), neg=0, invalid=96777 0286: dt=0.007000, rms=0.536 (0.003%), neg=0, invalid=96777 0287: dt=0.007000, rms=0.536 (0.005%), neg=0, invalid=96777 0288: dt=0.007000, rms=0.536 (0.010%), neg=0, invalid=96777 0289: dt=0.007000, rms=0.536 (0.009%), neg=0, invalid=96777 0290: dt=0.112000, rms=0.536 (0.034%), neg=0, invalid=96777 0291: dt=0.028000, rms=0.536 (0.016%), neg=0, invalid=96777 0292: dt=0.000875, rms=0.536 (-0.002%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0293: dt=0.000000, rms=0.533 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0294: dt=129.472000, rms=0.533 (0.187%), neg=0, invalid=96777 0295: dt=2.023000, rms=0.532 (0.001%), neg=0, invalid=96777 0296: dt=2.023000, rms=0.532 (0.001%), neg=0, invalid=96777 0297: dt=2.023000, rms=0.532 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.533, neg=0, invalid=96777 0298: dt=31.104000, rms=0.532 (0.097%), neg=0, invalid=96777 0299: dt=62.208000, rms=0.531 (0.154%), neg=0, invalid=96777 0300: dt=82.944000, rms=0.531 (0.118%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0301: dt=82.944000, rms=0.531 (-0.097%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=96777 0302: dt=36.288000, rms=0.528 (0.423%), neg=0, invalid=96777 0303: dt=20.736000, rms=0.528 (0.102%), neg=0, invalid=96777 0304: dt=20.736000, rms=0.527 (0.101%), neg=0, invalid=96777 0305: dt=20.736000, rms=0.527 (0.136%), neg=0, invalid=96777 0306: dt=20.736000, rms=0.526 (0.176%), neg=0, invalid=96777 0307: dt=20.736000, rms=0.525 (0.152%), neg=0, invalid=96777 0308: dt=20.736000, rms=0.524 (0.150%), neg=0, invalid=96777 0309: dt=20.736000, rms=0.523 (0.149%), neg=0, invalid=96777 0310: dt=20.736000, rms=0.523 (0.129%), neg=0, invalid=96777 0311: dt=20.736000, rms=0.522 (0.113%), neg=0, invalid=96777 0312: dt=20.736000, rms=0.522 (0.074%), neg=0, invalid=96777 0313: dt=62.208000, rms=0.521 (0.040%), neg=0, invalid=96777 0314: dt=62.208000, rms=0.521 (-0.063%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.522, neg=0, invalid=96777 iter 0, gcam->neg = 13 after 7 iterations, nbhd size=1, neg = 0 0315: dt=32.000000, rms=0.519 (0.609%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0316: dt=9.408805, rms=0.517 (0.323%), neg=0, invalid=96777 0317: dt=8.000000, rms=0.516 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0318: dt=8.000000, rms=0.515 (0.203%), neg=0, invalid=96777 0319: dt=8.000000, rms=0.514 (0.215%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0320: dt=8.000000, rms=0.513 (0.252%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 0321: dt=8.000000, rms=0.512 (0.223%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0322: dt=8.000000, rms=0.510 (0.332%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0323: dt=8.000000, rms=0.508 (0.280%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 15 iterations, nbhd size=2, neg = 0 0324: dt=8.000000, rms=0.507 (0.205%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 1 iterations, nbhd size=0, neg = 0 0325: dt=8.000000, rms=0.507 (0.145%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0326: dt=8.000000, rms=0.506 (0.128%), neg=0, invalid=96777 0327: dt=8.000000, rms=0.505 (0.248%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0328: dt=8.000000, rms=0.504 (0.203%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0329: dt=8.000000, rms=0.503 (0.189%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0330: dt=8.000000, rms=0.502 (0.147%), neg=0, invalid=96777 0331: dt=8.000000, rms=0.501 (0.130%), neg=0, invalid=96777 0332: dt=8.000000, rms=0.500 (0.211%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0333: dt=8.000000, rms=0.500 (0.106%), neg=0, invalid=96777 0334: dt=8.000000, rms=0.499 (0.142%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0335: dt=8.000000, rms=0.499 (0.072%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 15 iterations, nbhd size=2, neg = 0 0336: dt=8.000000, rms=0.498 (0.066%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0337: dt=11.200000, rms=0.498 (0.083%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0338: dt=25.600000, rms=0.498 (0.047%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 27 iterations, nbhd size=4, neg = 0 0339: dt=25.600000, rms=0.498 (-0.082%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 22 iterations, nbhd size=3, neg = 0 0340: dt=25.600000, rms=0.495 (0.525%), neg=0, invalid=96777 0341: dt=7.312500, rms=0.494 (0.191%), neg=0, invalid=96777 0342: dt=7.312500, rms=0.494 (0.116%), neg=0, invalid=96777 0343: dt=7.312500, rms=0.493 (0.129%), neg=0, invalid=96777 0344: dt=7.312500, rms=0.492 (0.164%), neg=0, invalid=96777 0345: dt=7.312500, rms=0.491 (0.146%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0346: dt=7.312500, rms=0.491 (0.122%), neg=0, invalid=96777 0347: dt=7.312500, rms=0.490 (0.124%), neg=0, invalid=96777 0348: dt=7.312500, rms=0.490 (0.086%), neg=0, invalid=96777 0349: dt=9.600000, rms=0.490 (0.011%), neg=0, invalid=96777 0350: dt=9.600000, rms=0.490 (0.028%), neg=0, invalid=96777 0351: dt=9.600000, rms=0.490 (0.013%), neg=0, invalid=96777 0352: dt=9.600000, rms=0.489 (0.014%), neg=0, invalid=96777 0353: dt=9.600000, rms=0.489 (0.021%), neg=0, invalid=96777 0354: dt=9.600000, rms=0.489 (0.029%), neg=0, invalid=96777 0355: dt=9.600000, rms=0.489 (0.026%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.496, neg=0, invalid=96777 0356: dt=1.008000, rms=0.496 (0.006%), neg=0, invalid=96777 0357: dt=0.432000, rms=0.496 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.496, neg=0, invalid=96777 iter 0, gcam->neg = 4 after 0 iterations, nbhd size=0, neg = 0 0358: dt=2.000000, rms=0.496 (0.026%), neg=0, invalid=96777 0359: dt=1.008000, rms=0.496 (0.009%), neg=0, invalid=96777 0360: dt=1.008000, rms=0.496 (0.028%), neg=0, invalid=96777 0361: dt=1.008000, rms=0.495 (0.026%), neg=0, invalid=96777 0362: dt=1.008000, rms=0.495 (0.007%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 0363: dt=0.004000, rms=0.506 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0364: dt=0.384000, rms=0.505 (0.024%), neg=0, invalid=96777 iter 0, gcam->neg = 10 after 7 iterations, nbhd size=1, neg = 0 0365: dt=0.272727, rms=0.505 (0.035%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0366: dt=0.478261, rms=0.505 (0.061%), neg=0, invalid=96777 0367: dt=0.080435, rms=0.505 (0.001%), neg=0, invalid=96777 0368: dt=0.080435, rms=0.505 (0.008%), neg=0, invalid=96777 0369: dt=0.080435, rms=0.505 (0.014%), neg=0, invalid=96777 0370: dt=0.080435, rms=0.505 (0.015%), neg=0, invalid=96777 0371: dt=0.080435, rms=0.505 (0.016%), neg=0, invalid=96777 0372: dt=0.080435, rms=0.505 (0.008%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0373: dt=0.080435, rms=0.505 (-0.014%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=96777 iter 0, gcam->neg = 1293 after 26 iterations, nbhd size=2, neg = 0 0374: dt=1.536000, rms=0.454 (7.953%), neg=0, invalid=96777 0375: dt=0.000000, rms=0.454 (-0.012%), neg=0, invalid=96777 iter 0, gcam->neg = 630 after 10 iterations, nbhd size=1, neg = 0 0376: dt=0.050000, rms=0.454 (-0.475%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.454, neg=0, invalid=96777 0377: dt=0.000000, rms=0.454 (0.000%), neg=0, invalid=96777 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 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 0378: dt=0.000000, rms=0.444 (-0.346%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 0379: dt=129.472000, rms=0.444 (0.062%), neg=0, invalid=96777 0380: dt=32.368000, rms=0.444 (0.004%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0381: dt=32.368000, rms=0.444 (0.001%), neg=0, invalid=96777 0382: dt=32.368000, rms=0.444 (-0.001%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 0383: dt=0.000000, rms=0.444 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0384: dt=36.288000, rms=0.444 (0.016%), neg=0, invalid=96777 0385: dt=36.288000, rms=0.444 (0.014%), neg=0, invalid=96777 0386: dt=36.288000, rms=0.444 (-0.008%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0387: dt=2.800000, rms=0.444 (0.019%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 14 iterations, nbhd size=2, neg = 0 0388: dt=11.200000, rms=0.444 (0.077%), neg=0, invalid=96777 0389: dt=0.400000, rms=0.444 (0.000%), neg=0, invalid=96777 0390: dt=0.400000, rms=0.444 (0.002%), neg=0, invalid=96777 0391: dt=0.400000, rms=0.444 (0.004%), neg=0, invalid=96777 0392: dt=0.400000, rms=0.444 (0.006%), neg=0, invalid=96777 0393: dt=0.400000, rms=0.444 (0.007%), neg=0, invalid=96777 0394: dt=0.400000, rms=0.444 (0.007%), neg=0, invalid=96777 0395: dt=0.400000, rms=0.444 (0.008%), neg=0, invalid=96777 0396: dt=0.400000, rms=0.444 (0.007%), neg=0, invalid=96777 0397: dt=0.400000, rms=0.444 (0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.444, neg=0, invalid=96777 iter 0, gcam->neg = 28 after 200 iterations, nbhd size=3, neg = 2 starting rms=0.010, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.005 (45.413%) iter 2, dt=0.000082: new neg 0, old_neg 1, delta 1, rms=0.003 (50.825%) 0398: dt=44.800000, rms=0.441 (0.554%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 16 iterations, nbhd size=2, neg = 0 0399: dt=25.600000, rms=0.441 (0.140%), neg=0, invalid=96777 iter 0, gcam->neg = 16 after 14 iterations, nbhd size=2, neg = 0 0400: dt=25.600000, rms=0.441 (-0.178%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 18 iterations, nbhd size=2, neg = 0 0401: dt=1.008000, rms=0.442 (0.020%), neg=0, invalid=96777 iter 0, gcam->neg = 48 after 17 iterations, nbhd size=2, neg = 0 0402: dt=2.304000, rms=0.442 (0.161%), neg=0, invalid=96777 0403: dt=0.003938, rms=0.442 (0.000%), neg=0, invalid=96777 0404: dt=0.003938, rms=0.442 (0.000%), neg=0, invalid=96777 0405: dt=0.003938, rms=0.442 (0.000%), neg=0, invalid=96777 0406: dt=0.003938, rms=0.442 (0.001%), neg=0, invalid=96777 0407: dt=0.003938, rms=0.442 (0.001%), neg=0, invalid=96777 0408: dt=0.003938, rms=0.442 (0.001%), neg=0, invalid=96777 0409: dt=0.003938, rms=0.442 (0.001%), neg=0, invalid=96777 0410: dt=0.003938, rms=0.442 (0.002%), neg=0, invalid=96777 0411: dt=0.003938, rms=0.442 (0.002%), neg=0, invalid=96777 0412: dt=0.003938, rms=0.442 (0.002%), neg=0, invalid=96777 0413: dt=0.003938, rms=0.442 (0.002%), neg=0, invalid=96777 0414: dt=0.003938, rms=0.442 (0.002%), neg=0, invalid=96777 0415: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0416: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0417: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0418: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0419: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0420: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0421: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0422: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0423: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0424: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0425: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0426: dt=0.003938, rms=0.442 (0.003%), neg=0, invalid=96777 0427: dt=0.003938, rms=0.441 (0.003%), neg=0, invalid=96777 0428: dt=0.003938, rms=0.441 (0.003%), neg=0, invalid=96777 0429: dt=0.003938, rms=0.441 (0.003%), neg=0, invalid=96777 0430: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0431: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0432: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0433: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0434: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0435: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0436: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0437: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0438: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0439: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 0440: dt=0.003938, rms=0.441 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.441, neg=0, invalid=96777 iter 0, gcam->neg = 228 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.010, neg=2, removing folds in lattice.... iter 1, dt=0.000023: new neg 1, old_neg 2, delta 1, rms=0.005 (47.290%) iter 2, dt=0.000082: new neg 0, old_neg 1, delta 1, rms=0.003 (51.399%) 0441: dt=10.830266, rms=0.438 (0.702%), neg=0, invalid=96777 0442: dt=0.252000, rms=0.438 (0.002%), neg=0, invalid=96777 0443: dt=0.252000, rms=0.438 (0.015%), neg=0, invalid=96777 0444: dt=0.252000, rms=0.438 (0.028%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0445: dt=0.252000, rms=0.438 (0.038%), neg=0, invalid=96777 0446: dt=0.252000, rms=0.438 (0.045%), neg=0, invalid=96777 0447: dt=0.252000, rms=0.437 (0.047%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0448: dt=0.252000, rms=0.437 (0.051%), neg=0, invalid=96777 0449: dt=0.252000, rms=0.437 (0.050%), neg=0, invalid=96777 0450: dt=0.252000, rms=0.437 (0.051%), neg=0, invalid=96777 0451: dt=0.252000, rms=0.437 (0.055%), neg=0, invalid=96777 0452: dt=0.252000, rms=0.436 (0.058%), neg=0, invalid=96777 0453: dt=0.252000, rms=0.436 (0.060%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0454: dt=0.252000, rms=0.436 (0.059%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 30 iterations, nbhd size=3, neg = 0 0455: dt=3.456000, rms=0.436 (0.034%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.440, neg=0, invalid=96777 0456: dt=0.000250, rms=0.440 (0.000%), neg=0, invalid=96777 0457: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.440, neg=0, invalid=96777 0458: dt=0.000000, rms=0.440 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.432, neg=0, invalid=96777 iter 0, gcam->neg = 337 after 31 iterations, nbhd size=3, neg = 0 0459: dt=0.397059, rms=0.423 (2.108%), neg=0, invalid=96777 0460: dt=0.000020, rms=0.423 (0.001%), neg=0, invalid=96777 0461: dt=0.000020, rms=0.423 (0.000%), neg=0, invalid=96777 0462: dt=0.000020, rms=0.423 (0.000%), neg=0, invalid=96777 0463: dt=0.000020, rms=0.423 (0.000%), neg=0, invalid=96777 0464: dt=0.000020, rms=0.423 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0465: dt=0.007000, rms=0.423 (0.006%), neg=0, invalid=96777 0466: dt=0.001500, rms=0.423 (0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=96777 iter 0, gcam->neg = 25 after 14 iterations, nbhd size=2, neg = 0 0467: dt=0.048000, rms=0.423 (0.135%), neg=0, invalid=96777 0468: dt=0.000012, rms=0.423 (0.001%), neg=0, invalid=96777 0469: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0470: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0471: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0472: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0473: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0474: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0475: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0476: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0477: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0478: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0479: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0480: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0481: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0482: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0483: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0484: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0485: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0486: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0487: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0488: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0489: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0490: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0491: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0492: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0493: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0494: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0495: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0496: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0497: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0498: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0499: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0500: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0501: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0502: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0503: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0504: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 0505: dt=0.000012, rms=0.423 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 9 minutes and 29 seconds. #-------------------------------------- #@# CA Reg Inv Mon Oct 13 16:54:37 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Mon Oct 13 16:55:35 CEST 2014 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10721726 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 59 seconds. #-------------------------------------- #@# SkullLTA Mon Oct 13 16:56:35 CEST 2014 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=5.0 skull bounding box = (48, 45, 13) --> (210, 241, 229) using (102, 110, 121) as brain centroid... mean wm in atlas = 126, using box (82,86,94) --> (121, 134,147) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.043 -0.028 0.050 -10.619; 0.005 1.029 0.520 -75.338; -0.075 -0.449 0.931 64.686; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.043 -0.028 0.050 -10.619; 0.005 1.029 0.520 -75.338; -0.075 -0.449 0.931 64.686; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.044 -0.062 0.033 -4.423; 0.040 1.029 0.513 -77.941; -0.075 -0.442 0.939 63.378; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.044 -0.062 0.033 -4.423; 0.040 1.026 0.511 -77.474; -0.075 -0.444 0.942 63.228; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04425 -0.06208 0.03340 -4.42313; 0.04001 1.02636 0.51146 -77.47422; -0.07513 -0.44357 0.94203 63.22775; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04425 -0.06208 0.03340 -4.42313; 0.04001 1.02636 0.51146 -77.47422; -0.07513 -0.44357 0.94203 63.22775; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.044 -0.062 0.033 -4.423; 0.040 1.026 0.511 -77.474; -0.075 -0.444 0.942 63.228; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.2) transform before final EM align: 1.044 -0.062 0.033 -4.423; 0.040 1.026 0.511 -77.474; -0.075 -0.444 0.942 63.228; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04425 -0.06208 0.03340 -4.42313; 0.04001 1.02636 0.51146 -77.47422; -0.07513 -0.44357 0.94203 63.22775; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04425 -0.06208 0.03340 -4.42313; 0.04001 1.02636 0.51146 -77.47422; -0.07513 -0.44357 0.94203 63.22775; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 4.3 tol 0.000000 final transform: 1.044 -0.062 0.033 -4.423; 0.040 1.026 0.511 -77.474; -0.075 -0.444 0.942 63.228; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 22 minutes and 58 seconds. #-------------------------------------- #@# SubCort Seg Mon Oct 13 17:19:33 CEST 2014 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname psyk-stud141.uio.no machine x86_64 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.30047 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (6498 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (6498 voxels, peak = 6), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.35399 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (9905 voxels, overlap=0.005) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (9905 voxels, peak = 4), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.08416 (107) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (202 voxels, overlap=0.834) Right_Pallidum (52): linear fit = 1.10 x + 0.0 (202 voxels, peak = 106), gca=106.2 gca peak = 0.18160 (96) mri peak = 0.11034 (107) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (435 voxels, overlap=0.661) Left_Pallidum (13): linear fit = 1.07 x + 0.0 (435 voxels, peak = 102), gca=102.2 gca peak = 0.27536 (62) mri peak = 0.07278 (51) Right_Hippocampus (53): linear fit = 0.81 x + 0.0 (873 voxels, overlap=0.036) Right_Hippocampus (53): linear fit = 0.81 x + 0.0 (873 voxels, peak = 50), gca=49.9 gca peak = 0.32745 (63) mri peak = 0.09275 (52) Left_Hippocampus (17): linear fit = 0.75 x + 0.0 (718 voxels, overlap=0.025) Left_Hippocampus (17): linear fit = 0.75 x + 0.0 (718 voxels, peak = 47), gca=46.9 gca peak = 0.08597 (105) mri peak = 0.09175 (111) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (42993 voxels, overlap=0.499) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (42993 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.08159 (108) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48027 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (48027 voxels, peak = 111), gca=110.8 gca peak = 0.07826 (63) mri peak = 0.04346 (42) Left_Cerebral_Cortex (3): linear fit = 0.69 x + 0.0 (19705 voxels, overlap=0.012) Left_Cerebral_Cortex (3): linear fit = 0.69 x + 0.0 (19705 voxels, peak = 44), gca=43.8 gca peak = 0.08598 (64) mri peak = 0.03867 (42) Right_Cerebral_Cortex (42): linear fit = 0.70 x + 0.0 (19341 voxels, overlap=0.002) Right_Cerebral_Cortex (42): linear fit = 0.70 x + 0.0 (19341 voxels, peak = 45), gca=45.1 gca peak = 0.24164 (71) mri peak = 0.08083 (68) Right_Caudate (50): linear fit = 0.95 x + 0.0 (436 voxels, overlap=0.811) Right_Caudate (50): linear fit = 0.95 x + 0.0 (436 voxels, peak = 68), gca=67.8 gca peak = 0.18227 (75) mri peak = 0.07493 (72) Left_Caudate (11): linear fit = 0.87 x + 0.0 (694 voxels, overlap=0.485) Left_Caudate (11): linear fit = 0.87 x + 0.0 (694 voxels, peak = 65), gca=64.9 gca peak = 0.10629 (62) mri peak = 0.04613 (46) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (22646 voxels, overlap=0.211) Left_Cerebellum_Cortex (8): linear fit = 0.80 x + 0.0 (22646 voxels, peak = 49), gca=49.3 gca peak = 0.11668 (59) mri peak = 0.04601 (49) Right_Cerebellum_Cortex (47): linear fit = 0.79 x + 0.0 (23317 voxels, overlap=0.128) Right_Cerebellum_Cortex (47): linear fit = 0.79 x + 0.0 (23317 voxels, peak = 46), gca=46.3 gca peak = 0.17849 (88) mri peak = 0.10129 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5876 voxels, overlap=0.253) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5876 voxels, peak = 95), gca=95.5 gca peak = 0.16819 (86) mri peak = 0.10090 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5557 voxels, overlap=0.424) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5557 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.13356 (55) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (295 voxels, overlap=0.342) Left_Amygdala (18): linear fit = 0.86 x + 0.0 (295 voxels, peak = 55), gca=54.7 gca peak = 0.42394 (62) mri peak = 0.11498 (54) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (309 voxels, overlap=0.480) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (309 voxels, peak = 56), gca=56.1 gca peak = 0.10041 (96) mri peak = 0.07204 (100) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3604 voxels, overlap=0.822) Left_Thalamus_Proper (10): linear fit = 1.03 x + 0.0 (3604 voxels, peak = 99), gca=99.4 gca peak = 0.13978 (88) mri peak = 0.06102 (97) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3077 voxels, overlap=0.873) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3077 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.05842 (78) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2433 voxels, overlap=0.819) Left_Putamen (12): linear fit = 0.95 x + 0.0 (2433 voxels, peak = 77), gca=77.4 gca peak = 0.09624 (82) mri peak = 0.04800 (83) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2530 voxels, overlap=0.863) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2530 voxels, peak = 80), gca=80.0 gca peak = 0.07543 (88) mri peak = 0.05521 (99) Brain_Stem (16): linear fit = 1.12 x + 0.0 (10788 voxels, overlap=0.568) Brain_Stem (16): linear fit = 1.12 x + 0.0 (10788 voxels, peak = 98), gca=98.1 gca peak = 0.12757 (95) mri peak = 0.08592 (109) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1142 voxels, overlap=0.226) Right_VentralDC (60): linear fit = 1.12 x + 0.0 (1142 voxels, peak = 107), gca=106.9 gca peak = 0.17004 (92) mri peak = 0.10174 (105) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1225 voxels, overlap=0.116) Left_VentralDC (28): linear fit = 1.12 x + 0.0 (1225 voxels, peak = 104), gca=103.5 gca peak = 0.21361 (36) mri peak = 0.16241 (11) Third_Ventricle (14): linear fit = 0.26 x + 0.0 (160 voxels, overlap=0.037) Third_Ventricle (14): linear fit = 0.26 x + 0.0 (160 voxels, peak = 10), gca=9.5 gca peak = 0.26069 (23) mri peak = 0.22616 ( 9) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (365 voxels, overlap=0.015) Fourth_Ventricle (15): linear fit = 0.31 x + 0.0 (365 voxels, peak = 7), gca=7.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.79 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.30047 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6498 voxels, overlap=0.463) Left_Lateral_Ventricle (4): linear fit = 0.52 x + 0.0 (6498 voxels, peak = 6), gca=5.8 gca peak = 0.29325 ( 9) mri peak = 0.35399 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (9905 voxels, overlap=0.713) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (9905 voxels, peak = 5), gca=5.2 gca peak = 0.22200 (107) mri peak = 0.08416 (107) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (202 voxels, overlap=1.023) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (202 voxels, peak = 107), gca=107.0 gca peak = 0.14938 (103) mri peak = 0.11034 (107) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (435 voxels, overlap=0.861) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (435 voxels, peak = 102), gca=102.5 gca peak = 0.32239 (50) mri peak = 0.07278 (51) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (873 voxels, overlap=1.010) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (873 voxels, peak = 50), gca=50.0 gca peak = 0.34901 (47) mri peak = 0.09275 (52) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (718 voxels, overlap=1.001) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (718 voxels, peak = 51), gca=50.5 gca peak = 0.08176 (110) mri peak = 0.09175 (111) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42993 voxels, overlap=0.710) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (42993 voxels, peak = 111), gca=110.6 gca peak = 0.08583 (111) mri peak = 0.08159 (108) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48027 voxels, overlap=0.743) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (48027 voxels, peak = 111), gca=111.0 gca peak = 0.10721 (44) mri peak = 0.04346 (42) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (19705 voxels, overlap=0.967) Left_Cerebral_Cortex (3): linear fit = 1.03 x + 0.0 (19705 voxels, peak = 46), gca=45.5 gca peak = 0.12294 (45) mri peak = 0.03867 (42) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (19341 voxels, overlap=0.862) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (19341 voxels, peak = 44), gca=43.9 gca peak = 0.27485 (70) mri peak = 0.08083 (68) Right_Caudate (50): linear fit = 1.00 x + 0.0 (436 voxels, overlap=1.014) Right_Caudate (50): linear fit = 1.00 x + 0.0 (436 voxels, peak = 70), gca=70.0 gca peak = 0.16597 (65) mri peak = 0.07493 (72) Left_Caudate (11): linear fit = 1.03 x + 0.0 (694 voxels, overlap=1.001) Left_Caudate (11): linear fit = 1.03 x + 0.0 (694 voxels, peak = 67), gca=67.3 gca peak = 0.13063 (49) mri peak = 0.04613 (46) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22646 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.98 x + 0.0 (22646 voxels, peak = 48), gca=47.8 gca peak = 0.15665 (47) mri peak = 0.04601 (49) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23317 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (23317 voxels, peak = 47), gca=47.0 gca peak = 0.16649 (96) mri peak = 0.10129 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5876 voxels, overlap=0.957) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5876 voxels, peak = 96), gca=95.5 gca peak = 0.15906 (93) mri peak = 0.10090 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5557 voxels, overlap=0.973) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5557 voxels, peak = 93), gca=93.0 gca peak = 0.35661 (54) mri peak = 0.13356 (55) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (295 voxels, overlap=1.003) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (295 voxels, peak = 54), gca=54.0 gca peak = 0.43477 (57) mri peak = 0.11498 (54) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (309 voxels, overlap=1.014) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (309 voxels, peak = 57), gca=57.0 gca peak = 0.09958 (96) mri peak = 0.07204 (100) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3604 voxels, overlap=0.937) Left_Thalamus_Proper (10): linear fit = 1.01 x + 0.0 (3604 voxels, peak = 97), gca=97.4 gca peak = 0.10873 (95) mri peak = 0.06102 (97) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3077 voxels, overlap=0.893) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3077 voxels, peak = 95), gca=95.5 gca peak = 0.09184 (77) mri peak = 0.05842 (78) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, overlap=1.001) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2433 voxels, peak = 77), gca=77.0 gca peak = 0.10426 (74) mri peak = 0.04800 (83) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2530 voxels, overlap=0.987) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2530 voxels, peak = 74), gca=73.6 gca peak = 0.06683 (95) mri peak = 0.05521 (99) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10788 voxels, overlap=0.880) Brain_Stem (16): linear fit = 1.00 x + 0.0 (10788 voxels, peak = 95), gca=94.5 gca peak = 0.10528 (102) mri peak = 0.08592 (109) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1142 voxels, overlap=0.804) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1142 voxels, peak = 102), gca=102.0 gca peak = 0.13290 (104) mri peak = 0.10174 (105) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1225 voxels, overlap=0.751) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1225 voxels, peak = 104), gca=104.0 gca peak = 0.35640 (14) mri peak = 0.16241 (11) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (160 voxels, overlap=0.152) Third_Ventricle (14): linear fit = 0.65 x + 0.0 (160 voxels, peak = 9), gca=9.2 gca peak = 0.33827 ( 9) mri peak = 0.22616 ( 9) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (365 voxels, overlap=0.762) Fourth_Ventricle (15): linear fit = 0.79 x + 0.0 (365 voxels, peak = 7), gca=7.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.33196 (26) gca peak Third_Ventricle = 0.35640 (14) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.44858 (60) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.24407 (60) gca peak Left_choroid_plexus = 0.09854 (54) gca peak Right_Inf_Lat_Vent = 0.30433 (26) gca peak Right_Accumbens_area = 0.30100 (69) gca peak Right_vessel = 0.31431 (59) gca peak Right_choroid_plexus = 0.11173 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.16099 (85) gca peak non_WM_hypointensities = 0.11076 (55) gca peak Optic_Chiasm = 0.34842 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.63 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 16185 gm and wm labels changed (% 8 to gray, %92 to white out of all changed labels) 382 hippocampal voxels changed. 5 amygdala voxels changed. pass 1: 105138 changed. image ll: -2.271, PF=1.000 pass 2: 22521 changed. image ll: -2.268, PF=1.000 pass 3: 9656 changed. pass 4: 4981 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 15 minutes and 3 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/cc_up.lta Andre_v_5_3 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/cc_up.lta reading aseg from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.auto_noCCseg.mgz reading norm from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/norm.mgz 45040 voxels in left wm, 35393 in right wm, xrange [124, 136] searching rotation angles z=[-4 10], y=[-4 10] searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.3 global minimum found at slice 131.0, rotations (2.90, 2.56) final transformation (x=131.0, yr=2.896, zr=2.564): 0.998 -0.045 0.050 -0.655; 0.045 0.999 0.002 -13.898; -0.051 0.000 0.999 54.721; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 132 138 eigenvectors: -0.001 -0.001 1.000; -0.345 -0.939 -0.002; 0.939 -0.345 0.001; writing aseg with callosum to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.8 minutes #-------------------------------------- #@# Merge ASeg Mon Oct 13 17:35:24 CEST 2014 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Mon Oct 13 17:35:24 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 5799 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 111 white matter peak found at 110 gm peak at 49 (49), valley at 29 (29) csf peak at 14, setting threshold to 37 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 50 (50), valley at 25 (25) csf peak at 14, setting threshold to 38 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 0 seconds. #-------------------------------------------- #@# Mask BFS Mon Oct 13 17:38:25 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1800915 voxels in mask (pct= 10.73) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Oct 13 17:38:27 CEST 2014 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (106.0): 106.6 +- 4.7 [80.0 --> 125.0] GM (68.0) : 67.0 +- 10.3 [30.0 --> 96.0] setting bottom of white matter range to 77.3 setting top of gray matter range to 87.6 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... 1634 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6694 filled 228 bright non-wm voxels segmented. 1089 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.55 minutes reading wm segmentation from wm.seg.mgz... 392 voxels added to wm to prevent paths from MTL structures to cortex 3351 additional wm voxels added 0 additional wm voxels added SEG EDIT: 100970 voxels turned on, 35724 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 101 new 101 115,126,128 old 101 new 101 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 24 found - 24 modified | TOTAL: 52 pass 2 (xy-): 0 found - 24 modified | TOTAL: 52 pass 1 (yz+): 42 found - 42 modified | TOTAL: 94 pass 2 (yz+): 0 found - 42 modified | TOTAL: 94 pass 1 (yz-): 23 found - 23 modified | TOTAL: 117 pass 2 (yz-): 0 found - 23 modified | TOTAL: 117 pass 1 (xz+): 29 found - 29 modified | TOTAL: 146 pass 2 (xz+): 0 found - 29 modified | TOTAL: 146 pass 1 (xz-): 27 found - 27 modified | TOTAL: 173 pass 2 (xz-): 0 found - 27 modified | TOTAL: 173 Iteration Number : 1 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 pass 1 (+++): 14 found - 14 modified | TOTAL: 22 pass 2 (+++): 0 found - 14 modified | TOTAL: 22 pass 1 (+++): 2 found - 2 modified | TOTAL: 24 pass 2 (+++): 0 found - 2 modified | TOTAL: 24 Iteration Number : 1 pass 1 (++): 54 found - 54 modified | TOTAL: 54 pass 2 (++): 0 found - 54 modified | TOTAL: 54 pass 1 (+-): 59 found - 59 modified | TOTAL: 113 pass 2 (+-): 0 found - 59 modified | TOTAL: 113 pass 1 (--): 46 found - 46 modified | TOTAL: 159 pass 2 (--): 0 found - 46 modified | TOTAL: 159 pass 1 (-+): 34 found - 34 modified | TOTAL: 193 pass 2 (-+): 0 found - 34 modified | TOTAL: 193 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 2 found - 2 modified | TOTAL: 7 pass 2 (xy-): 0 found - 2 modified | TOTAL: 7 pass 1 (yz+): 1 found - 1 modified | TOTAL: 8 pass 2 (yz+): 0 found - 1 modified | TOTAL: 8 pass 1 (yz-): 2 found - 2 modified | TOTAL: 10 pass 2 (yz-): 0 found - 2 modified | TOTAL: 10 pass 1 (xz+): 2 found - 2 modified | TOTAL: 12 pass 2 (xz+): 0 found - 2 modified | TOTAL: 12 pass 1 (xz-): 3 found - 3 modified | TOTAL: 15 pass 2 (xz-): 0 found - 3 modified | TOTAL: 15 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 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 3 found - 3 modified | TOTAL: 7 pass 2 (--): 0 found - 3 modified | TOTAL: 7 pass 1 (-+): 0 found - 0 modified | TOTAL: 7 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 2 found - 2 modified | TOTAL: 2 pass 2 (xy-): 0 found - 2 modified | TOTAL: 2 pass 1 (yz+): 0 found - 0 modified | TOTAL: 2 pass 1 (yz-): 1 found - 1 modified | TOTAL: 3 pass 2 (yz-): 0 found - 1 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 = 415 (out of 649388: 0.063906) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Mon Oct 13 17:40:26 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.023 -0.061 0.033 -1.789; 0.034 0.979 0.568 -76.064; -0.073 -0.490 0.846 83.376; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1740 (min = 350, max = 1400), aspect = 0.50 (min = 0.10, max = 0.75) need search nearby using seed (126, 109, 86), TAL = (2.0, -42.0, 19.0) talairach voxel to voxel transform 0.973 0.031 -0.059 8.988; -0.062 0.763 -0.510 100.438; 0.048 0.444 0.882 -39.651; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 109, 86) --> (2.0, -42.0, 19.0) done. writing output to filled.mgz... filling took 0.7 minutes talairach cc position changed to (2.00, -42.00, 19.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -42.00, 19.00) SRC: (112.39, 132.98, 89.85) search lh wm seed point around talairach space (-16.00, -42.00, 19.00), SRC: (147.40, 130.75, 91.59) 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 Mon Oct 13 17:41:06 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 0 found - 3 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 4 found - 4 modified | TOTAL: 13 pass 2 (xz-): 0 found - 4 modified | TOTAL: 13 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 (--): 0 found - 0 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 = 16 (out of 307272: 0.005207) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 297 vertices, 355 faces slice 50: 5172 vertices, 5404 faces slice 60: 14606 vertices, 14972 faces slice 70: 26603 vertices, 26957 faces slice 80: 38044 vertices, 38406 faces slice 90: 48378 vertices, 48743 faces slice 100: 58436 vertices, 58792 faces slice 110: 68990 vertices, 69350 faces slice 120: 78881 vertices, 79237 faces slice 130: 88260 vertices, 88611 faces slice 140: 97325 vertices, 97675 faces slice 150: 106328 vertices, 106662 faces slice 160: 113824 vertices, 114124 faces slice 170: 121318 vertices, 121581 faces slice 180: 127375 vertices, 127588 faces slice 190: 132226 vertices, 132392 faces slice 200: 134519 vertices, 134552 faces slice 210: 134560 vertices, 134580 faces slice 220: 134560 vertices, 134580 faces slice 230: 134560 vertices, 134580 faces slice 240: 134560 vertices, 134580 faces slice 250: 134560 vertices, 134580 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 134560 voxel in cpt #1: X=-20 [v=134560,e=403740,f=269160] located at (-29.715368, -17.678999, 5.375751) For the whole surface: X=-20 [v=134560,e=403740,f=269160] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Oct 13 17:41:12 CEST 2014 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Oct 13 17:41:15 CEST 2014 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts avg radius = 50.1 mm, total surface area = 73874 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.093 (target=0.015) step 005: RMS=0.069 (target=0.015) step 010: RMS=0.051 (target=0.015) step 015: RMS=0.042 (target=0.015) step 020: RMS=0.037 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Oct 13 17:41:44 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.58 (0.00-->7.79) (max @ vno 104317 --> 104318) face area 0.03 +- 0.04 (-0.05-->0.99) scaling brain by 0.326... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.055, avgs=0 005/300: dt: 0.9000, rms radial error=174.801, avgs=0 010/300: dt: 0.9000, rms radial error=174.255, avgs=0 015/300: dt: 0.9000, rms radial error=173.539, avgs=0 020/300: dt: 0.9000, rms radial error=172.722, avgs=0 025/300: dt: 0.9000, rms radial error=171.848, avgs=0 030/300: dt: 0.9000, rms radial error=170.942, avgs=0 035/300: dt: 0.9000, rms radial error=170.019, avgs=0 040/300: dt: 0.9000, rms radial error=169.088, avgs=0 045/300: dt: 0.9000, rms radial error=168.154, avgs=0 050/300: dt: 0.9000, rms radial error=167.220, avgs=0 055/300: dt: 0.9000, rms radial error=166.288, avgs=0 060/300: dt: 0.9000, rms radial error=165.359, avgs=0 065/300: dt: 0.9000, rms radial error=164.433, avgs=0 070/300: dt: 0.9000, rms radial error=163.512, avgs=0 075/300: dt: 0.9000, rms radial error=162.594, avgs=0 080/300: dt: 0.9000, rms radial error=161.681, avgs=0 085/300: dt: 0.9000, rms radial error=160.772, avgs=0 090/300: dt: 0.9000, rms radial error=159.867, avgs=0 095/300: dt: 0.9000, rms radial error=158.967, avgs=0 100/300: dt: 0.9000, rms radial error=158.071, avgs=0 105/300: dt: 0.9000, rms radial error=157.179, avgs=0 110/300: dt: 0.9000, rms radial error=156.292, avgs=0 115/300: dt: 0.9000, rms radial error=155.410, avgs=0 120/300: dt: 0.9000, rms radial error=154.532, avgs=0 125/300: dt: 0.9000, rms radial error=153.662, avgs=0 130/300: dt: 0.9000, rms radial error=152.796, avgs=0 135/300: dt: 0.9000, rms radial error=151.935, avgs=0 140/300: dt: 0.9000, rms radial error=151.079, avgs=0 145/300: dt: 0.9000, rms radial error=150.227, avgs=0 150/300: dt: 0.9000, rms radial error=149.380, avgs=0 155/300: dt: 0.9000, rms radial error=148.538, avgs=0 160/300: dt: 0.9000, rms radial error=147.701, avgs=0 165/300: dt: 0.9000, rms radial error=146.868, avgs=0 170/300: dt: 0.9000, rms radial error=146.041, avgs=0 175/300: dt: 0.9000, rms radial error=145.218, avgs=0 180/300: dt: 0.9000, rms radial error=144.399, avgs=0 185/300: dt: 0.9000, rms radial error=143.586, avgs=0 190/300: dt: 0.9000, rms radial error=142.777, avgs=0 195/300: dt: 0.9000, rms radial error=141.973, avgs=0 200/300: dt: 0.9000, rms radial error=141.174, avgs=0 205/300: dt: 0.9000, rms radial error=140.379, avgs=0 210/300: dt: 0.9000, rms radial error=139.588, avgs=0 215/300: dt: 0.9000, rms radial error=138.802, avgs=0 220/300: dt: 0.9000, rms radial error=138.020, avgs=0 225/300: dt: 0.9000, rms radial error=137.243, avgs=0 230/300: dt: 0.9000, rms radial error=136.470, avgs=0 235/300: dt: 0.9000, rms radial error=135.701, avgs=0 240/300: dt: 0.9000, rms radial error=134.937, avgs=0 245/300: dt: 0.9000, rms radial error=134.177, avgs=0 250/300: dt: 0.9000, rms radial error=133.421, avgs=0 255/300: dt: 0.9000, rms radial error=132.669, avgs=0 260/300: dt: 0.9000, rms radial error=131.922, avgs=0 265/300: dt: 0.9000, rms radial error=131.179, avgs=0 270/300: dt: 0.9000, rms radial error=130.440, avgs=0 275/300: dt: 0.9000, rms radial error=129.705, avgs=0 280/300: dt: 0.9000, rms radial error=128.974, avgs=0 285/300: dt: 0.9000, rms radial error=128.248, avgs=0 290/300: dt: 0.9000, rms radial error=127.525, avgs=0 295/300: dt: 0.9000, rms radial error=126.808, avgs=0 300/300: dt: 0.9000, rms radial error=126.095, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15378.45 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00014 epoch 2 (K=40.0), pass 1, starting sse = 2467.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 234.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00985 epoch 4 (K=640.0), pass 1, starting sse = 11.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/16 = 0.01118 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Oct 13 17:45:43 CEST 2014 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Andre_v_5_3 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-20 (nv=134560, nf=269160, ne=403740, g=11) 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... 1427 ambiguous faces found in tessellation segmenting defects... 22 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 10 -merging segment 13 into 12 -merging segment 16 into 15 19 defects to be corrected 0 vertices coincident reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4968 (-4.7484) -vertex loglikelihood: -6.7019 (-3.3510) -normal dot loglikelihood: -3.6671 (-3.6671) -quad curv loglikelihood: -6.3081 (-3.1540) Total Loglikelihood : -26.1739 CORRECTING DEFECT 0 (vertices=37, convex hull=49) After retessellation of defect 0, euler #=-19 (133652,400522,266851) : difference with theory (-16) = 3 CORRECTING DEFECT 1 (vertices=5, convex hull=24) After retessellation of defect 1, euler #=-18 (133654,400535,266863) : difference with theory (-15) = 3 CORRECTING DEFECT 2 (vertices=33, convex hull=47) After retessellation of defect 2, euler #=-17 (133663,400581,266901) : difference with theory (-14) = 3 CORRECTING DEFECT 3 (vertices=21, convex hull=27) After retessellation of defect 3, euler #=-16 (133667,400598,266915) : difference with theory (-13) = 3 CORRECTING DEFECT 4 (vertices=68, convex hull=94) After retessellation of defect 4, euler #=-15 (133705,400754,267034) : difference with theory (-12) = 3 CORRECTING DEFECT 5 (vertices=11, convex hull=31) After retessellation of defect 5, euler #=-14 (133707,400768,267047) : difference with theory (-11) = 3 CORRECTING DEFECT 6 (vertices=47, convex hull=90) After retessellation of defect 6, euler #=-13 (133741,400908,267154) : difference with theory (-10) = 3 CORRECTING DEFECT 7 (vertices=50, convex hull=88) After retessellation of defect 7, euler #=-12 (133775,401048,267261) : difference with theory (-9) = 3 CORRECTING DEFECT 8 (vertices=6, convex hull=17) After retessellation of defect 8, euler #=-11 (133776,401056,267269) : difference with theory (-8) = 3 CORRECTING DEFECT 9 (vertices=17, convex hull=12) After retessellation of defect 9, euler #=-10 (133777,401061,267274) : difference with theory (-7) = 3 CORRECTING DEFECT 10 (vertices=84, convex hull=100) After retessellation of defect 10, euler #=-8 (133806,401198,267384) : difference with theory (-6) = 2 CORRECTING DEFECT 11 (vertices=205, convex hull=76) After retessellation of defect 11, euler #=-6 (133824,401287,267457) : difference with theory (-5) = 1 CORRECTING DEFECT 12 (vertices=82, convex hull=41) After retessellation of defect 12, euler #=-5 (133836,401338,267497) : difference with theory (-4) = 1 CORRECTING DEFECT 13 (vertices=103, convex hull=146) After retessellation of defect 13, euler #=-3 (133887,401555,267665) : difference with theory (-3) = 0 CORRECTING DEFECT 14 (vertices=12, convex hull=26) After retessellation of defect 14, euler #=-2 (133890,401573,267681) : difference with theory (-2) = 0 CORRECTING DEFECT 15 (vertices=50, convex hull=80) After retessellation of defect 15, euler #=-1 (133899,401632,267732) : difference with theory (-1) = 0 CORRECTING DEFECT 16 (vertices=32, convex hull=77) After retessellation of defect 16, euler #=0 (133919,401721,267802) : difference with theory (0) = 0 CORRECTING DEFECT 17 (vertices=27, convex hull=49) After retessellation of defect 17, euler #=1 (133930,401776,267847) : difference with theory (1) = 0 CORRECTING DEFECT 18 (vertices=30, convex hull=26) After retessellation of defect 18, euler #=2 (133935,401799,267866) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.06-->10.22) (max @ vno 100459 --> 106413) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.21 (0.06-->10.22) (max @ vno 100459 --> 106413) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 66 mutations (34.9%), 123 crossovers (65.1%), 24 vertices were eliminated building final representation... 625 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133935, nf=267866, ne=401799, g=0) writing corrected surface to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 9.2 minutes 0 defective edges removing intersecting faces 000: 97 intersecting 001: 13 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 133935 - 401799 + 267866 = 2 --> 0 holes F =2V-4: 267866 = 267870-4 (0) 2E=3F: 803598 = 803598 (0) total defect index = 0 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 11 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Mon Oct 13 17:54:58 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Andre_v_5_3 lh only generating white matter surface 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.06-->3.71) (max @ vno 100459 --> 106413) face area 0.29 +- 0.12 (0.00-->1.27) mean absolute distance = 0.79 +- 0.96 3732 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=69.0, 141 (141) missing vertices, mean dist 0.5 [0.7 (%22.4)->0.8 (%77.6))] %62 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.94 +- 0.27 (0.10-->3.80) (max @ vno 99295 --> 98376) face area 0.29 +- 0.14 (0.00-->1.80) mean absolute distance = 0.34 +- 0.72 2389 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7893194.5, rms=15.12 001: dt: 0.5000, sse=6890662.0, rms=11.436 (0.000%) 002: dt: 0.5000, sse=6502553.0, rms=8.930 (0.000%) 003: dt: 0.5000, sse=6544945.5, rms=7.172 (0.000%) 004: dt: 0.5000, sse=6584281.0, rms=6.012 (0.000%) 005: dt: 0.5000, sse=6821105.5, rms=5.264 (0.000%) 006: dt: 0.5000, sse=6875603.0, rms=4.846 (0.000%) 007: dt: 0.5000, sse=7063183.5, rms=4.574 (0.000%) 008: dt: 0.5000, sse=7048645.0, rms=4.446 (0.000%) 009: dt: 0.5000, sse=7149175.0, rms=4.334 (0.000%) rms = 4.30, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7072522.0, rms=4.299 (0.000%) 011: dt: 0.2500, sse=4333780.5, rms=2.806 (0.000%) 012: dt: 0.2500, sse=3779535.2, rms=2.371 (0.000%) 013: dt: 0.2500, sse=3559957.2, rms=2.223 (0.000%) 014: dt: 0.2500, sse=3462123.5, rms=2.129 (0.000%) 015: dt: 0.2500, sse=3404501.5, rms=2.067 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3361674.2, rms=2.020 (0.000%) 017: dt: 0.1250, sse=3244662.8, rms=1.883 (0.000%) rms = 1.86, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3218014.8, rms=1.862 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=72.2, 71 (46) missing vertices, mean dist -0.2 [0.4 (%70.0)->0.3 (%30.0))] %69 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.12-->4.02) (max @ vno 99295 --> 98376) face area 0.37 +- 0.17 (0.00-->2.40) mean absolute distance = 0.29 +- 0.53 2879 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3942435.0, rms=5.17 019: dt: 0.5000, sse=4416411.0, rms=3.517 (0.000%) rms = 4.06, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3938319.0, rms=2.472 (0.000%) 021: dt: 0.2500, sse=3733147.5, rms=1.986 (0.000%) 022: dt: 0.2500, sse=3626347.5, rms=1.722 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3589711.8, rms=1.681 (0.000%) 024: dt: 0.1250, sse=3502921.2, rms=1.553 (0.000%) rms = 1.53, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3472130.2, rms=1.534 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=75.2, 66 (42) missing vertices, mean dist -0.2 [0.3 (%68.5)->0.2 (%31.5))] %76 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.26 (0.13-->4.29) (max @ vno 99295 --> 98376) face area 0.36 +- 0.17 (0.00-->2.54) mean absolute distance = 0.24 +- 0.41 2277 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3828535.8, rms=4.14 026: dt: 0.5000, sse=4287982.0, rms=3.539 (0.000%) rms = 3.88, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3869751.2, rms=2.327 (0.000%) 028: dt: 0.2500, sse=3685069.2, rms=1.837 (0.000%) 029: dt: 0.2500, sse=3671205.2, rms=1.532 (0.000%) rms = 1.53, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3661117.5, rms=1.529 (0.000%) 031: dt: 0.1250, sse=3588980.0, rms=1.364 (0.000%) rms = 1.34, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3567281.5, rms=1.345 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group mean border=76.4, 58 (39) missing vertices, mean dist -0.1 [0.3 (%56.8)->0.2 (%43.2))] %80 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3632608.0, rms=2.21 rms = 2.64, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3722592.8, rms=1.526 (0.000%) 034: dt: 0.2500, sse=3903157.5, rms=1.093 (0.000%) rms = 1.04, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=3950884.2, rms=1.045 (0.000%) rms = 1.03, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=3985472.5, rms=1.027 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 14 non-cortical segments detected only using segment with 2223 vertices erasing segment 1 (vno[0] = 78380) erasing segment 2 (vno[0] = 79385) erasing segment 3 (vno[0] = 81163) erasing segment 4 (vno[0] = 84073) erasing segment 5 (vno[0] = 84998) erasing segment 6 (vno[0] = 87822) erasing segment 7 (vno[0] = 88545) erasing segment 8 (vno[0] = 96661) erasing segment 9 (vno[0] = 96677) erasing segment 10 (vno[0] = 100397) erasing segment 11 (vno[0] = 101311) erasing segment 12 (vno[0] = 102174) erasing segment 13 (vno[0] = 105490) writing cortex label to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.cortex.label... writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv writing smoothed area to lh.area writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area vertex spacing 0.92 +- 0.26 (0.08-->4.34) (max @ vno 98376 --> 99295) face area 0.36 +- 0.16 (0.00-->2.54) refinement took 5.2 minutes #-------------------------------------------- #@# Smooth2 lh Mon Oct 13 18:00:12 CEST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts 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 Mon Oct 13 18:00:15 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 50.4 mm, total surface area = 86885 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.056 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.016 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 188 vertices thresholded to be in k1 ~ [-6.85 0.29], k2 ~ [-0.13 0.32] total integrated curvature = 0.448*4pi (5.632) --> 1 handles ICI = 1.5, FI = 10.1, variation=169.886 113 vertices thresholded to be in [-0.05 0.03] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 68 vertices thresholded to be in [-1.01 0.15] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Mon Oct 13 18:02:00 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.327954 WARN: S explicit min: 0.000000 vertex = 144 #-------------------------------------------- #@# Sphere lh Mon Oct 13 18:02:04 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.53 pass 1: epoch 2 of 3 starting distance error %19.55 unfolding complete - removing small folds... starting distance error %19.46 removing remaining folds... final distance error %19.48 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.79 hours #-------------------------------------------- #@# Surf Reg lh Mon Oct 13 18:49:12 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.602 curvature mean = 0.041, std = 0.932 curvature mean = 0.008, std = 0.869 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 307117.9, tmin=0.8942 d=32.00 min @ (0.00, 8.00, 0.00) sse = 226073.8, tmin=1.7943 d=16.00 min @ (0.00, 0.00, 4.00) sse = 211214.2, tmin=2.6997 d=4.00 min @ (1.00, 0.00, -1.00) sse = 210319.8, tmin=4.5306 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 209823.5, tmin=5.4561 d=1.00 min @ (0.00, 0.25, 0.25) sse = 209721.6, tmin=6.3801 d=0.50 min @ (0.00, 0.00, -0.12) sse = 209715.5, tmin=7.3190 tol=1.0e+00, sigma=0.5, host=psyk-, 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 7.32 min curvature mean = 0.022, std = 0.950 curvature mean = 0.004, std = 0.946 curvature mean = 0.019, std = 0.961 curvature mean = 0.002, std = 0.976 curvature mean = 0.018, std = 0.964 curvature mean = 0.000, std = 0.990 2 Reading smoothwm curvature mean = -0.019, std = 0.253 curvature mean = 0.005, std = 0.067 curvature mean = 0.043, std = 0.380 curvature mean = 0.005, std = 0.079 curvature mean = 0.027, std = 0.580 curvature mean = 0.005, std = 0.086 curvature mean = 0.015, std = 0.719 curvature mean = 0.005, std = 0.088 curvature mean = 0.005, std = 0.823 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 1113: 33 negative triangles #-------------------------------------------- #@# Jacobian white lh Mon Oct 13 19:21:34 CEST 2014 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Mon Oct 13 19:21:36 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Oct 13 19:21:38 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1458 labels changed using aseg relabeling using gibbs priors... 000: 2902 changed, 133935 examined... 001: 673 changed, 12460 examined... 002: 171 changed, 3779 examined... 003: 43 changed, 1038 examined... 004: 15 changed, 278 examined... 005: 6 changed, 101 examined... 006: 0 changed, 40 examined... 255 labels changed using aseg 000: 108 total segments, 67 labels (266 vertices) changed 001: 43 total segments, 4 labels (12 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 847 vertices marked for relabeling... 847 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 47 seconds. #-------------------------------------------- #@# Make Pial Surf lh Mon Oct 13 19:22:25 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.06-->3.71) (max @ vno 100459 --> 106413) face area 0.29 +- 0.12 (0.00-->1.27) mean absolute distance = 0.79 +- 0.96 3792 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 130 points - only 14.62% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 831 points - only 0.00% unknown deleting segment 5 with 45 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown deleting segment 7 with 40 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 49 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown mean border=69.0, 141 (141) missing vertices, mean dist 0.5 [0.7 (%22.6)->0.8 (%77.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.94 +- 0.27 (0.10-->3.15) (max @ vno 69317 --> 69300) face area 0.29 +- 0.14 (0.00-->1.64) mean absolute distance = 0.34 +- 0.72 2450 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7931433.0, rms=15.08 001: dt: 0.5000, sse=6935160.0, rms=11.406 (0.000%) 002: dt: 0.5000, sse=6544342.5, rms=8.907 (0.000%) 003: dt: 0.5000, sse=6586972.0, rms=7.155 (0.000%) 004: dt: 0.5000, sse=6627329.5, rms=5.998 (0.000%) 005: dt: 0.5000, sse=6865879.0, rms=5.255 (0.000%) 006: dt: 0.5000, sse=6919816.5, rms=4.836 (0.000%) 007: dt: 0.5000, sse=7114851.5, rms=4.565 (0.000%) 008: dt: 0.5000, sse=7097618.5, rms=4.438 (0.000%) 009: dt: 0.5000, sse=7203923.0, rms=4.325 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7126259.0, rms=4.290 (0.000%) 011: dt: 0.2500, sse=4362082.0, rms=2.797 (0.000%) 012: dt: 0.2500, sse=3801983.2, rms=2.360 (0.000%) 013: dt: 0.2500, sse=3582298.0, rms=2.212 (0.000%) 014: dt: 0.2500, sse=3481731.8, rms=2.118 (0.000%) 015: dt: 0.2500, sse=3421952.2, rms=2.059 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3381572.5, rms=2.015 (0.000%) 017: dt: 0.1250, sse=3263632.2, rms=1.881 (0.000%) rms = 1.86, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3235483.2, rms=1.861 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 161 points - only 17.39% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 4 with 645 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 20 points - only 0.00% unknown deleting segment 9 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown deleting segment 13 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 16 with 61 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown mean border=72.2, 79 (46) missing vertices, mean dist -0.2 [0.4 (%70.0)->0.3 (%30.0))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.12-->3.28) (max @ vno 93103 --> 92209) face area 0.37 +- 0.17 (0.00-->1.96) mean absolute distance = 0.29 +- 0.53 2944 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3970987.0, rms=5.17 019: dt: 0.5000, sse=4454506.0, rms=3.513 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3973708.8, rms=2.475 (0.000%) 021: dt: 0.2500, sse=3767152.8, rms=1.990 (0.000%) 022: dt: 0.2500, sse=3656728.5, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3623260.8, rms=1.686 (0.000%) 024: dt: 0.1250, sse=3536692.2, rms=1.560 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3505861.5, rms=1.540 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 168 points - only 16.67% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 686 points - only 0.00% unknown deleting segment 4 with 40 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 57 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown mean border=75.1, 77 (43) missing vertices, mean dist -0.2 [0.3 (%68.3)->0.2 (%31.7))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.13-->3.56) (max @ vno 111457 --> 111456) face area 0.36 +- 0.16 (0.00-->2.01) mean absolute distance = 0.25 +- 0.41 2338 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3865593.2, rms=4.13 026: dt: 0.5000, sse=4328042.5, rms=3.538 (0.000%) rms = 3.87, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3907882.5, rms=2.334 (0.000%) 028: dt: 0.2500, sse=3723624.5, rms=1.850 (0.000%) 029: dt: 0.2500, sse=3709880.0, rms=1.549 (0.000%) rms = 1.55, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3699352.5, rms=1.545 (0.000%) 031: dt: 0.1250, sse=3626586.0, rms=1.384 (0.000%) rms = 1.36, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3604916.5, rms=1.365 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 175 points - only 16.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 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 712 points - only 0.00% unknown deleting segment 5 with 44 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 60 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown mean border=76.3, 81 (39) missing vertices, mean dist -0.1 [0.3 (%56.8)->0.2 (%43.2))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3669868.8, rms=2.21 rms = 2.63, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3762752.2, rms=1.531 (0.000%) 034: dt: 0.2500, sse=3948763.2, rms=1.104 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=3999052.2, rms=1.059 (0.000%) rms = 1.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4031869.2, rms=1.039 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 25.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=44.7, 108 (108) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.0 (%100.0))] %14 local maxima, %66 large gradients and %15 min vals, 1713 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27774222.0, rms=31.55 001: dt: 0.5000, sse=19744250.0, rms=26.075 (0.000%) 002: dt: 0.5000, sse=14127545.0, rms=21.462 (0.000%) 003: dt: 0.5000, sse=10548771.0, rms=17.785 (0.000%) 004: dt: 0.5000, sse=8627045.0, rms=14.803 (0.000%) 005: dt: 0.5000, sse=7348371.5, rms=12.299 (0.000%) 006: dt: 0.5000, sse=6612727.0, rms=10.273 (0.000%) 007: dt: 0.5000, sse=6053383.0, rms=8.576 (0.000%) 008: dt: 0.5000, sse=5788639.0, rms=7.187 (0.000%) 009: dt: 0.5000, sse=5610497.5, rms=6.077 (0.000%) 010: dt: 0.5000, sse=5643526.5, rms=5.275 (0.000%) 011: dt: 0.5000, sse=5587664.0, rms=4.732 (0.000%) 012: dt: 0.5000, sse=5703336.0, rms=4.397 (0.000%) 013: dt: 0.5000, sse=5683819.0, rms=4.153 (0.000%) 014: dt: 0.5000, sse=5771044.0, rms=3.999 (0.000%) 015: dt: 0.5000, sse=5726464.5, rms=3.881 (0.000%) 016: dt: 0.5000, sse=5811575.0, rms=3.800 (0.000%) 017: dt: 0.5000, sse=5761283.5, rms=3.730 (0.000%) 018: dt: 0.5000, sse=5797567.0, rms=3.675 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5756588.5, rms=3.635 (0.000%) 020: dt: 0.2500, sse=3891133.2, rms=2.857 (0.000%) 021: dt: 0.2500, sse=3675003.8, rms=2.687 (0.000%) rms = 2.64, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3579567.8, rms=2.641 (0.000%) 023: dt: 0.1250, sse=3450344.5, rms=2.556 (0.000%) rms = 2.55, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3435661.8, rms=2.546 (0.000%) positioning took 2.1 minutes mean border=42.7, 472 (28) missing vertices, mean dist 0.2 [0.2 (%54.3)->0.8 (%45.7))] %33 local maxima, %51 large gradients and %11 min vals, 605 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4060163.5, rms=4.82 025: dt: 0.5000, sse=4331332.5, rms=3.821 (0.000%) 026: dt: 0.5000, sse=5401962.0, rms=3.678 (0.000%) 027: dt: 0.5000, sse=5601610.0, rms=3.578 (0.000%) rms = 3.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4500867.0, rms=2.911 (0.000%) 029: dt: 0.2500, sse=4218836.0, rms=2.637 (0.000%) 030: dt: 0.2500, sse=4089517.2, rms=2.547 (0.000%) rms = 2.51, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4061397.5, rms=2.515 (0.000%) 032: dt: 0.1250, sse=3957642.5, rms=2.438 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3947623.5, rms=2.426 (0.000%) positioning took 0.8 minutes mean border=40.4, 678 (23) missing vertices, mean dist 0.2 [0.2 (%43.4)->0.5 (%56.6))] %51 local maxima, %33 large gradients and %10 min vals, 678 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4268281.0, rms=4.13 034: dt: 0.5000, sse=4423501.5, rms=3.341 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4168684.0, rms=2.780 (0.000%) 036: dt: 0.2500, sse=4205171.5, rms=2.458 (0.000%) 037: dt: 0.2500, sse=4173098.5, rms=2.378 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4184372.2, rms=2.341 (0.000%) 039: dt: 0.1250, sse=4097827.0, rms=2.291 (0.000%) rms = 2.28, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4094593.8, rms=2.283 (0.000%) positioning took 0.7 minutes mean border=38.8, 1433 (17) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %61 local maxima, %22 large gradients and %10 min vals, 636 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4201795.5, rms=3.02 rms = 3.05, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4079617.0, rms=2.582 (0.000%) 042: dt: 0.2500, sse=4110240.2, rms=2.267 (0.000%) 043: dt: 0.2500, sse=4164422.8, rms=2.161 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4187721.8, rms=2.118 (0.000%) rms = 2.07, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4126205.8, rms=2.073 (0.000%) positioning took 0.5 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area.pial vertex spacing 1.03 +- 0.42 (0.08-->7.11) (max @ vno 99529 --> 98590) face area 0.43 +- 0.31 (0.00-->8.42) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed thickness calculation complete, 568:1039 truncations. 39591 vertices at 0 distance 100082 vertices at 1 distance 77896 vertices at 2 distance 25453 vertices at 3 distance 6940 vertices at 4 distance 2124 vertices at 5 distance 713 vertices at 6 distance 268 vertices at 7 distance 106 vertices at 8 distance 52 vertices at 9 distance 45 vertices at 10 distance 28 vertices at 11 distance 18 vertices at 12 distance 16 vertices at 13 distance 7 vertices at 14 distance 12 vertices at 15 distance 6 vertices at 16 distance 2 vertices at 17 distance 7 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.thickness positioning took 10.4 minutes #-------------------------------------------- #@# Surf Volume lh Mon Oct 13 19:32:49 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Mon Oct 13 19:32:49 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts pctsurfcon --s Andre_v_5_3 --lh-only Log file is /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts/pctsurfcon.log Mon Oct 13 19:32:49 CEST 2014 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux psyk-stud141.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.wm.mgh --regheader Andre_v_5_3 --cortex srcvol = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz as target reference. Loading label /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.cortex.label Reading surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 = 80449 Masking with /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.cortex.label Writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.wm.mgh Dim: 133935 1 1 mri_vol2surf --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.gm.mgh --projfrac 0.3 --regheader Andre_v_5_3 --cortex srcvol = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz as target reference. Loading label /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.cortex.label Reading surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Done reading source surface Reading thickness /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 = 90496 Masking with /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.cortex.label Writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.gm.mgh Dim: 133935 1 1 mri_concat /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.wm.mgh /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.40099/lh.gm.mgh --paired-diff-norm --mul 100 --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.w-g.pct.mgh mri_segstats --in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.w-g.pct.mgh --annot Andre_v_5_3 lh aparc --sum /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.w-g.pct.mgh --annot Andre_v_5_3 lh aparc --sum /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/stats/lh.w-g.pct.stats --snr sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.w-g.pct.mgh Vertex Area is 0.704441 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1454 1009.554 2 1002 caudalanteriorcingulate 887 647.045 3 1003 caudalmiddlefrontal 3870 2733.591 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1632 1139.993 6 1006 entorhinal 480 367.502 7 1007 fusiform 4801 3442.580 8 1008 inferiorparietal 6309 4472.915 9 1009 inferiortemporal 4514 3308.535 10 1010 isthmuscingulate 1739 1208.767 11 1011 lateraloccipital 7020 4995.259 12 1012 lateralorbitofrontal 3176 2363.671 13 1013 lingual 4532 3284.443 14 1014 medialorbitofrontal 2129 1573.339 15 1015 middletemporal 4475 3346.282 16 1016 parahippocampal 1156 820.563 17 1017 paracentral 2071 1368.520 18 1018 parsopercularis 2305 1652.782 19 1019 parsorbitalis 785 601.243 20 1020 parstriangularis 1990 1419.133 21 1021 pericalcarine 1559 1057.552 22 1022 postcentral 6931 4797.041 23 1023 posteriorcingulate 2184 1532.488 24 1024 precentral 7744 5094.454 25 1025 precuneus 5126 3620.595 26 1026 rostralanteriorcingulate 988 675.354 27 1027 rostralmiddlefrontal 7318 5331.572 28 1028 superiorfrontal 10543 7588.846 29 1029 superiorparietal 8260 5910.164 30 1030 superiortemporal 6031 4167.248 31 1031 supramarginal 7163 4992.788 32 1032 frontalpole 287 238.902 33 1033 temporalpole 757 633.756 34 1034 transversetemporal 686 489.783 35 1035 insula 3054 2046.179 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Mon Oct 13 19:32:57 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Andre_v_5_3 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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 1454 1010 3288 2.824 0.698 0.147 0.051 21 3.0 bankssts 887 647 1373 1.974 0.653 0.135 0.026 12 1.0 caudalanteriorcingulate 3870 2734 6470 2.119 0.571 0.118 0.025 34 4.1 caudalmiddlefrontal 1632 1140 2304 1.793 0.392 0.148 0.038 20 2.6 cuneus 480 368 1557 3.074 0.893 0.116 0.019 3 0.4 entorhinal 4801 3443 9633 2.336 0.705 0.140 0.042 69 8.2 fusiform 6309 4473 10256 2.072 0.596 0.136 0.053 204 12.7 inferiorparietal 4514 3309 9640 2.416 0.820 0.143 0.050 71 8.7 inferiortemporal 1739 1209 3252 2.475 0.934 0.136 0.051 28 3.5 isthmuscingulate 7020 4995 9931 1.826 0.486 0.152 0.042 93 11.8 lateraloccipital 3176 2364 6308 2.345 0.615 0.147 0.050 45 6.3 lateralorbitofrontal 4532 3284 7266 2.032 0.681 0.150 0.050 64 9.1 lingual 2129 1573 3988 2.198 0.883 0.153 0.062 35 4.5 medialorbitofrontal 4475 3346 10742 2.610 0.706 0.153 0.056 83 10.3 middletemporal 1156 821 2435 2.494 0.859 0.091 0.017 7 0.7 parahippocampal 2071 1369 2732 1.845 0.615 0.094 0.019 12 1.7 paracentral 2305 1653 4227 2.326 0.482 0.127 0.034 27 2.9 parsopercularis 785 601 1922 2.355 0.731 0.171 0.076 14 1.8 parsorbitalis 1990 1419 3898 2.336 0.570 0.129 0.029 21 2.4 parstriangularis 1559 1058 1725 1.660 0.455 0.144 0.048 20 3.0 pericalcarine 6931 4797 8929 1.717 0.627 0.124 0.033 75 9.2 postcentral 2184 1532 3454 2.166 0.651 0.144 0.050 33 3.6 posteriorcingulate 7744 5094 12090 2.179 0.611 0.109 0.033 69 9.1 precentral 5126 3621 9041 2.257 0.681 0.133 0.039 65 8.3 precuneus 988 675 1957 2.430 0.843 0.147 0.049 20 1.9 rostralanteriorcingulate 7318 5332 12027 1.922 0.632 0.152 0.053 138 14.9 rostralmiddlefrontal 10543 7589 19969 2.214 0.674 0.128 0.034 118 14.1 superiorfrontal 8260 5910 11448 1.783 0.479 0.137 0.037 106 12.2 superiorparietal 6031 4167 11275 2.368 0.699 0.114 0.032 58 7.5 superiortemporal 7163 4993 12774 2.371 0.565 0.130 0.039 99 11.5 supramarginal 287 239 696 2.184 0.539 0.237 0.108 10 1.3 frontalpole 757 634 3196 3.283 0.987 0.192 0.068 20 1.9 temporalpole 686 490 1087 2.072 0.552 0.116 0.028 5 0.7 transversetemporal 3054 2046 6784 3.239 0.953 0.098 0.033 23 2.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Oct 13 19:33:10 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 61 labels changed using aseg relabeling using gibbs priors... 000: 9251 changed, 133935 examined... 001: 2220 changed, 35245 examined... 002: 628 changed, 11493 examined... 003: 304 changed, 3562 examined... 004: 150 changed, 1695 examined... 005: 86 changed, 841 examined... 006: 46 changed, 451 examined... 007: 25 changed, 258 examined... 008: 9 changed, 146 examined... 009: 7 changed, 58 examined... 010: 1 changed, 25 examined... 011: 1 changed, 5 examined... 012: 0 changed, 5 examined... 10 labels changed using aseg 000: 253 total segments, 173 labels (2510 vertices) changed 001: 93 total segments, 13 labels (47 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 141 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 416 vertices marked for relabeling... 416 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 53 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Oct 13 19:34:03 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -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 Andre_v_5_3 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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 923 667 1543 1.894 0.581 0.161 0.074 28 2.5 G_and_S_frontomargin 1556 1116 2204 1.832 0.463 0.151 0.043 20 2.6 G_and_S_occipital_inf 1533 985 1964 1.729 0.633 0.104 0.026 12 1.6 G_and_S_paracentral 1553 1192 3182 2.495 0.730 0.149 0.042 22 2.6 G_and_S_subcentral 672 525 1487 2.181 0.598 0.201 0.075 20 2.0 G_and_S_transv_frontopol 2432 1711 4654 2.292 0.779 0.142 0.049 38 4.2 G_and_S_cingul-Ant 1410 1039 2293 2.058 0.549 0.120 0.022 13 1.2 G_and_S_cingul-Mid-Ant 1448 1036 2327 2.136 0.506 0.116 0.027 12 1.7 G_and_S_cingul-Mid-Post 629 480 1622 2.765 0.593 0.185 0.067 13 1.6 G_cingul-Post-dorsal 358 221 756 2.780 1.294 0.152 0.067 8 0.9 G_cingul-Post-ventral 1478 1025 2223 1.824 0.416 0.158 0.047 22 2.8 G_cuneus 1229 903 2847 2.516 0.527 0.146 0.045 21 2.1 G_front_inf-Opercular 239 167 648 2.764 0.456 0.137 0.028 4 0.3 G_front_inf-Orbital 1217 898 2913 2.481 0.565 0.155 0.041 20 2.0 G_front_inf-Triangul 4133 3088 8382 2.180 0.651 0.160 0.051 77 8.4 G_front_middle 7114 5132 14628 2.311 0.664 0.137 0.039 88 10.9 G_front_sup 449 315 1221 3.558 0.755 0.103 0.029 5 0.5 G_Ins_lg_and_S_cent_ins 650 411 2301 3.953 0.755 0.095 0.048 7 0.6 G_insular_short 2045 1458 3582 2.028 0.465 0.159 0.050 33 4.0 G_occipital_middle 1703 1182 2373 1.810 0.467 0.146 0.037 23 2.6 G_occipital_sup 1980 1413 4709 2.557 0.623 0.148 0.044 35 3.7 G_oc-temp_lat-fusifor 3025 2242 5111 1.950 0.701 0.162 0.054 48 6.9 G_oc-temp_med-Lingual 1174 879 3481 2.894 0.926 0.110 0.022 10 1.0 G_oc-temp_med-Parahip 2109 1667 5318 2.448 0.602 0.188 0.077 46 6.2 G_orbital 2123 1558 4170 2.109 0.596 0.157 0.060 41 5.1 G_pariet_inf-Angular 3513 2525 7639 2.522 0.490 0.143 0.051 67 7.3 G_pariet_inf-Supramar 2927 2218 5172 1.920 0.484 0.154 0.051 50 5.7 G_parietal_sup 2603 1838 3610 1.687 0.444 0.145 0.045 40 4.5 G_postcentral 2870 1800 5315 2.395 0.550 0.112 0.045 35 4.0 G_precentral 2703 1982 5831 2.381 0.697 0.152 0.058 50 5.8 G_precuneus 883 748 2216 2.317 0.638 0.205 0.090 23 3.1 G_rectus 18 8 18 1.961 0.456 0.067 0.013 0 0.0 G_subcallosal 485 342 856 2.085 0.421 0.115 0.026 4 0.5 G_temp_sup-G_T_transv 2264 1605 5542 2.608 0.711 0.141 0.047 33 4.1 G_temp_sup-Lateral 546 398 1368 2.902 0.899 0.104 0.028 4 0.5 G_temp_sup-Plan_polar 1083 741 1847 2.268 0.527 0.095 0.020 6 0.9 G_temp_sup-Plan_tempo 2364 1837 6338 2.665 0.836 0.173 0.080 55 6.5 G_temporal_inf 2481 1932 6573 2.641 0.669 0.174 0.067 58 7.5 G_temporal_middle 470 307 628 2.222 0.494 0.098 0.018 3 0.3 Lat_Fis-ant-Horizont 323 230 476 2.110 0.444 0.121 0.022 2 0.3 Lat_Fis-ant-Vertical 1656 1105 2230 2.456 0.592 0.119 0.032 14 2.1 Lat_Fis-post 2317 1720 3536 1.795 0.536 0.167 0.046 35 4.3 Pole_occipital 1699 1366 6138 2.931 0.970 0.188 0.068 42 4.6 Pole_temporal 2076 1430 2649 1.942 0.740 0.128 0.045 22 3.3 S_calcarine 3082 2015 3037 1.609 0.624 0.092 0.020 14 2.5 S_central 1226 862 1638 1.967 0.644 0.104 0.021 9 1.0 S_cingul-Marginalis 465 335 850 2.728 0.693 0.091 0.017 2 0.3 S_circular_insula_ant 1613 1117 2518 2.637 1.018 0.075 0.012 5 0.9 S_circular_insula_inf 1763 1196 2420 2.398 0.588 0.099 0.026 9 1.5 S_circular_insula_sup 901 628 1283 2.084 0.762 0.106 0.025 7 0.9 S_collat_transv_ant 489 332 511 1.801 0.441 0.136 0.037 5 0.7 S_collat_transv_post 2414 1685 3214 1.852 0.483 0.105 0.024 16 2.1 S_front_inf 1324 934 1869 1.765 0.649 0.133 0.043 21 2.1 S_front_middle 2705 1920 3454 1.800 0.503 0.097 0.019 16 2.1 S_front_sup 699 452 762 1.802 0.490 0.100 0.025 6 0.8 S_interm_prim-Jensen 3006 2055 3429 1.816 0.545 0.122 0.041 131 4.3 S_intrapariet_and_P_trans 1055 719 1164 1.756 0.398 0.121 0.029 8 1.2 S_oc_middle_and_Lunatus 1328 913 1474 1.760 0.421 0.127 0.029 14 1.5 S_oc_sup_and_transversal 561 393 635 1.665 0.425 0.105 0.023 5 0.5 S_occipital_ant 1059 742 1411 2.004 0.655 0.113 0.027 8 1.1 S_oc-temp_lat 2335 1602 3473 2.253 0.635 0.110 0.024 16 2.3 S_oc-temp_med_and_Lingual 359 250 508 1.854 0.467 0.126 0.029 3 0.4 S_orbital_lateral 534 373 760 2.085 0.971 0.099 0.018 3 0.4 S_orbital_med-olfact 1127 790 1745 2.057 0.589 0.132 0.055 13 2.1 S_orbital-H_Shaped 1471 1008 1887 1.940 0.576 0.118 0.029 12 1.7 S_parieto_occipital 1609 991 1420 1.788 0.716 0.125 0.040 26 2.6 S_pericallosal 3865 2625 4571 1.805 0.514 0.117 0.028 35 4.5 S_postcentral 1826 1243 2668 2.122 0.459 0.103 0.022 13 1.6 S_precentral-inf-part 1537 1061 1826 1.918 0.621 0.119 0.027 10 1.8 S_precentral-sup-part 533 358 928 2.643 1.142 0.131 0.044 6 0.7 S_suborbital 1155 782 1772 2.321 0.503 0.115 0.028 9 1.3 S_subparietal 1385 943 2059 2.217 0.613 0.115 0.028 12 1.6 S_temporal_inf 5667 3904 9981 2.403 0.722 0.128 0.041 83 9.5 S_temporal_sup 400 266 484 2.054 0.623 0.107 0.016 2 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Mon Oct 13 19:34:16 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1228 labels changed using aseg relabeling using gibbs priors... 000: 2786 changed, 133935 examined... 001: 691 changed, 11803 examined... 002: 164 changed, 3792 examined... 003: 81 changed, 944 examined... 004: 29 changed, 453 examined... 005: 15 changed, 192 examined... 006: 7 changed, 105 examined... 007: 7 changed, 50 examined... 008: 7 changed, 39 examined... 009: 0 changed, 34 examined... 187 labels changed using aseg 000: 66 total segments, 33 labels (312 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 29 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 641 vertices marked for relabeling... 641 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Mon Oct 13 19:35:03 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab Andre_v_5_3 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 1677 1192 2676 2.063 0.666 0.127 0.027 21 1.9 caudalanteriorcingulate 3946 2796 6669 2.127 0.569 0.118 0.026 35 4.1 caudalmiddlefrontal 2329 1600 3126 1.790 0.417 0.143 0.037 28 3.5 cuneus 454 345 1481 3.101 0.919 0.114 0.018 3 0.3 entorhinal 4433 3152 8495 2.324 0.690 0.135 0.037 59 6.7 fusiform 6117 4326 9891 2.075 0.600 0.135 0.046 97 11.2 inferiorparietal 4648 3472 10667 2.444 0.843 0.153 0.056 84 10.2 inferiortemporal 1751 1212 3244 2.464 0.945 0.135 0.050 28 3.5 isthmuscingulate 7363 5243 10352 1.809 0.488 0.152 0.042 97 12.3 lateraloccipital 3265 2431 6518 2.279 0.646 0.163 0.065 68 8.4 lateralorbitofrontal 4530 3286 7266 2.032 0.679 0.150 0.051 64 9.1 lingual 1875 1402 3468 2.135 0.870 0.155 0.059 31 4.1 medialorbitofrontal 5612 4114 13020 2.587 0.724 0.148 0.052 96 12.0 middletemporal 1144 815 2435 2.506 0.857 0.091 0.017 7 0.7 parahippocampal 2389 1586 3265 1.899 0.634 0.094 0.019 14 1.9 paracentral 2063 1467 3830 2.378 0.491 0.129 0.036 25 2.7 parsopercularis 917 664 1935 2.358 0.631 0.124 0.028 9 1.1 parsorbitalis 2374 1706 4570 2.293 0.554 0.132 0.031 26 3.0 parstriangularis 1561 1057 1726 1.661 0.456 0.143 0.049 20 2.9 pericalcarine 7673 5324 9966 1.737 0.635 0.124 0.034 82 10.3 postcentral 2253 1582 3515 2.155 0.643 0.142 0.049 33 3.6 posteriorcingulate 7677 5035 11933 2.193 0.604 0.109 0.033 68 9.1 precentral 5119 3623 9237 2.274 0.669 0.134 0.040 68 8.3 precuneus 1310 892 2517 2.439 0.849 0.145 0.059 24 2.5 rostralanteriorcingulate 5318 3911 8941 1.941 0.645 0.153 0.054 89 10.7 rostralmiddlefrontal 11153 8111 21177 2.168 0.683 0.135 0.038 145 16.6 superiorfrontal 6628 4782 9216 1.787 0.465 0.140 0.044 190 11.2 superiorparietal 8003 5648 16847 2.502 0.774 0.124 0.038 93 11.7 superiortemporal 6992 4851 12354 2.376 0.560 0.130 0.039 98 11.3 supramarginal 656 468 1044 2.076 0.547 0.116 0.028 5 0.7 transversetemporal 2726 1840 6294 3.285 0.975 0.090 0.030 18 2.2 insula #-------------------------------------------- #@# Tessellate rh Mon Oct 13 19:35:16 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.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-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 2 found - 2 modified | TOTAL: 7 pass 2 (yz+): 0 found - 2 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 4 found - 4 modified | TOTAL: 13 pass 2 (xz+): 0 found - 4 modified | TOTAL: 13 pass 1 (xz-): 7 found - 7 modified | TOTAL: 20 pass 2 (xz-): 0 found - 7 modified | TOTAL: 20 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 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 1 found - 1 modified | TOTAL: 5 pass 2 (+-): 0 found - 1 modified | TOTAL: 5 pass 1 (--): 2 found - 2 modified | TOTAL: 7 pass 2 (--): 0 found - 2 modified | TOTAL: 7 pass 1 (-+): 1 found - 1 modified | TOTAL: 8 pass 2 (-+): 0 found - 1 modified | TOTAL: 8 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 = 28 (out of 319915: 0.008752) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 802 vertices, 926 faces slice 50: 7688 vertices, 7998 faces slice 60: 19500 vertices, 19968 faces slice 70: 32275 vertices, 32670 faces slice 80: 43999 vertices, 44382 faces slice 90: 54567 vertices, 54928 faces slice 100: 64148 vertices, 64521 faces slice 110: 74380 vertices, 74773 faces slice 120: 84611 vertices, 84980 faces slice 130: 93939 vertices, 94301 faces slice 140: 102863 vertices, 103199 faces slice 150: 111348 vertices, 111644 faces slice 160: 118111 vertices, 118381 faces slice 170: 125059 vertices, 125282 faces slice 180: 130735 vertices, 130937 faces slice 190: 134447 vertices, 134594 faces slice 200: 135984 vertices, 136016 faces slice 210: 135984 vertices, 136016 faces slice 220: 135984 vertices, 136016 faces slice 230: 135984 vertices, 136016 faces slice 240: 135984 vertices, 136016 faces slice 250: 135984 vertices, 136016 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 135976 voxel in cpt #1: X=-34 [v=135976,e=408030,f=272020] located at (28.144863, -22.144989, 3.912389) 8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (0.000000, -22.000000, 4.000000) For the whole surface: X=-32 [v=135984,e=408048,f=272032] 2 components have been found keeping component #1 with 135976 vertices done #-------------------------------------------- #@# Smooth1 rh Mon Oct 13 19:35:22 CEST 2014 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Oct 13 19:35:25 CEST 2014 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts avg radius = 51.0 mm, total surface area = 74869 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.5 minutes Not saving sulc step 000: RMS=0.095 (target=0.015) step 005: RMS=0.071 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.026 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Oct 13 19:35:54 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.98 +- 0.57 (0.00-->7.31) (max @ vno 107059 --> 107922) face area 0.03 +- 0.04 (-0.16-->0.75) scaling brain by 0.326... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=174.576, avgs=0 005/300: dt: 0.9000, rms radial error=174.327, avgs=0 010/300: dt: 0.9000, rms radial error=173.783, avgs=0 015/300: dt: 0.9000, rms radial error=173.068, avgs=0 020/300: dt: 0.9000, rms radial error=172.255, avgs=0 025/300: dt: 0.9000, rms radial error=171.383, avgs=0 030/300: dt: 0.9000, rms radial error=170.479, avgs=0 035/300: dt: 0.9000, rms radial error=169.558, avgs=0 040/300: dt: 0.9000, rms radial error=168.629, avgs=0 045/300: dt: 0.9000, rms radial error=167.698, avgs=0 050/300: dt: 0.9000, rms radial error=166.766, avgs=0 055/300: dt: 0.9000, rms radial error=165.837, avgs=0 060/300: dt: 0.9000, rms radial error=164.910, avgs=0 065/300: dt: 0.9000, rms radial error=163.988, avgs=0 070/300: dt: 0.9000, rms radial error=163.069, avgs=0 075/300: dt: 0.9000, rms radial error=162.155, avgs=0 080/300: dt: 0.9000, rms radial error=161.245, avgs=0 085/300: dt: 0.9000, rms radial error=160.339, avgs=0 090/300: dt: 0.9000, rms radial error=159.437, avgs=0 095/300: dt: 0.9000, rms radial error=158.540, avgs=0 100/300: dt: 0.9000, rms radial error=157.648, avgs=0 105/300: dt: 0.9000, rms radial error=156.760, avgs=0 110/300: dt: 0.9000, rms radial error=155.877, avgs=0 115/300: dt: 0.9000, rms radial error=154.998, avgs=0 120/300: dt: 0.9000, rms radial error=154.124, avgs=0 125/300: dt: 0.9000, rms radial error=153.254, avgs=0 130/300: dt: 0.9000, rms radial error=152.389, avgs=0 135/300: dt: 0.9000, rms radial error=151.529, avgs=0 140/300: dt: 0.9000, rms radial error=150.675, avgs=0 145/300: dt: 0.9000, rms radial error=149.827, avgs=0 150/300: dt: 0.9000, rms radial error=148.984, avgs=0 155/300: dt: 0.9000, rms radial error=148.146, avgs=0 160/300: dt: 0.9000, rms radial error=147.312, avgs=0 165/300: dt: 0.9000, rms radial error=146.483, avgs=0 170/300: dt: 0.9000, rms radial error=145.659, avgs=0 175/300: dt: 0.9000, rms radial error=144.839, avgs=0 180/300: dt: 0.9000, rms radial error=144.024, avgs=0 185/300: dt: 0.9000, rms radial error=143.214, avgs=0 190/300: dt: 0.9000, rms radial error=142.408, avgs=0 195/300: dt: 0.9000, rms radial error=141.607, avgs=0 200/300: dt: 0.9000, rms radial error=140.810, avgs=0 205/300: dt: 0.9000, rms radial error=140.018, avgs=0 210/300: dt: 0.9000, rms radial error=139.230, avgs=0 215/300: dt: 0.9000, rms radial error=138.446, avgs=0 220/300: dt: 0.9000, rms radial error=137.667, avgs=0 225/300: dt: 0.9000, rms radial error=136.893, avgs=0 230/300: dt: 0.9000, rms radial error=136.123, avgs=0 235/300: dt: 0.9000, rms radial error=135.357, avgs=0 240/300: dt: 0.9000, rms radial error=134.596, avgs=0 245/300: dt: 0.9000, rms radial error=133.840, avgs=0 250/300: dt: 0.9000, rms radial error=133.088, avgs=0 255/300: dt: 0.9000, rms radial error=132.340, avgs=0 260/300: dt: 0.9000, rms radial error=131.596, avgs=0 265/300: dt: 0.9000, rms radial error=130.856, avgs=0 270/300: dt: 0.9000, rms radial error=130.121, avgs=0 275/300: dt: 0.9000, rms radial error=129.389, avgs=0 280/300: dt: 0.9000, rms radial error=128.662, avgs=0 285/300: dt: 0.9000, rms radial error=127.939, avgs=0 290/300: dt: 0.9000, rms radial error=127.220, avgs=0 295/300: dt: 0.9000, rms radial error=126.505, avgs=0 300/300: dt: 0.9000, rms radial error=125.793, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15543.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 2 (K=40.0), pass 1, starting sse = 2500.37 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00022 epoch 3 (K=160.0), pass 1, starting sse = 245.94 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00986 epoch 4 (K=640.0), pass 1, starting sse = 14.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/15 = 0.01179 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.07 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Oct 13 19:39:52 CEST 2014 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Andre_v_5_3 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 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-34 (nv=135976, nf=272020, ne=408030, g=18) 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 8 iterations marking ambiguous vertices... 2773 ambiguous faces found in tessellation segmenting defects... 28 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 28 defects to be corrected 0 vertices coincident reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5096 (-4.7548) -vertex loglikelihood: -6.7596 (-3.3798) -normal dot loglikelihood: -3.6119 (-3.6119) -quad curv loglikelihood: -6.1475 (-3.0737) Total Loglikelihood : -26.0286 CORRECTING DEFECT 0 (vertices=32, convex hull=63) After retessellation of defect 0, euler #=-25 (134294,402257,267938) : difference with theory (-25) = 0 CORRECTING DEFECT 1 (vertices=40, convex hull=78) After retessellation of defect 1, euler #=-24 (134305,402322,267993) : difference with theory (-24) = 0 CORRECTING DEFECT 2 (vertices=415, convex hull=171) After retessellation of defect 2, euler #=-23 (134314,402436,268099) : difference with theory (-23) = 0 CORRECTING DEFECT 3 (vertices=28, convex hull=23) After retessellation of defect 3, euler #=-22 (134316,402447,268109) : difference with theory (-22) = 0 CORRECTING DEFECT 4 (vertices=6, convex hull=39) After retessellation of defect 4, euler #=-21 (134318,402463,268124) : difference with theory (-21) = 0 CORRECTING DEFECT 5 (vertices=52, convex hull=27) After retessellation of defect 5, euler #=-20 (134322,402483,268141) : difference with theory (-20) = 0 CORRECTING DEFECT 6 (vertices=21, convex hull=53) After retessellation of defect 6, euler #=-19 (134334,402535,268182) : difference with theory (-19) = 0 CORRECTING DEFECT 7 (vertices=12, convex hull=26) After retessellation of defect 7, euler #=-18 (134338,402551,268195) : difference with theory (-18) = 0 CORRECTING DEFECT 8 (vertices=8, convex hull=30) After retessellation of defect 8, euler #=-17 (134341,402568,268210) : difference with theory (-17) = 0 CORRECTING DEFECT 9 (vertices=33, convex hull=59) After retessellation of defect 9, euler #=-16 (134350,402616,268250) : difference with theory (-16) = 0 CORRECTING DEFECT 10 (vertices=27, convex hull=49) After retessellation of defect 10, euler #=-15 (134359,402659,268285) : difference with theory (-15) = 0 CORRECTING DEFECT 11 (vertices=312, convex hull=238) After retessellation of defect 11, euler #=-14 (134441,403021,268566) : difference with theory (-14) = 0 CORRECTING DEFECT 12 (vertices=5, convex hull=21) After retessellation of defect 12, euler #=-13 (134442,403029,268574) : difference with theory (-13) = 0 CORRECTING DEFECT 13 (vertices=13, convex hull=13) After retessellation of defect 13, euler #=-12 (134444,403037,268581) : difference with theory (-12) = 0 CORRECTING DEFECT 14 (vertices=177, convex hull=61) After retessellation of defect 14, euler #=-11 (134465,403134,268658) : difference with theory (-11) = 0 CORRECTING DEFECT 15 (vertices=15, convex hull=35) After retessellation of defect 15, euler #=-10 (134467,403152,268675) : difference with theory (-10) = 0 CORRECTING DEFECT 16 (vertices=25, convex hull=27) After retessellation of defect 16, euler #=-9 (134470,403169,268690) : difference with theory (-9) = 0 CORRECTING DEFECT 17 (vertices=22, convex hull=30) After retessellation of defect 17, euler #=-8 (134473,403187,268706) : difference with theory (-8) = 0 CORRECTING DEFECT 18 (vertices=25, convex hull=35) After retessellation of defect 18, euler #=-7 (134478,403216,268731) : difference with theory (-7) = 0 CORRECTING DEFECT 19 (vertices=5, convex hull=24) After retessellation of defect 19, euler #=-6 (134480,403229,268743) : difference with theory (-6) = 0 CORRECTING DEFECT 20 (vertices=21, convex hull=33) After retessellation of defect 20, euler #=-5 (134483,403248,268760) : difference with theory (-5) = 0 CORRECTING DEFECT 21 (vertices=58, convex hull=61) After retessellation of defect 21, euler #=-4 (134497,403314,268813) : difference with theory (-4) = 0 CORRECTING DEFECT 22 (vertices=73, convex hull=49) After retessellation of defect 22, euler #=-3 (134504,403360,268853) : difference with theory (-3) = 0 CORRECTING DEFECT 23 (vertices=5, convex hull=13) After retessellation of defect 23, euler #=-2 (134505,403365,268858) : difference with theory (-2) = 0 CORRECTING DEFECT 24 (vertices=136, convex hull=109) After retessellation of defect 24, euler #=-1 (134549,403545,268995) : difference with theory (-1) = 0 CORRECTING DEFECT 25 (vertices=37, convex hull=63) After retessellation of defect 25, euler #=0 (134558,403595,269037) : difference with theory (0) = 0 CORRECTING DEFECT 26 (vertices=49, convex hull=91) After retessellation of defect 26, euler #=1 (134574,403682,269109) : difference with theory (1) = 0 CORRECTING DEFECT 27 (vertices=41, convex hull=86) After retessellation of defect 27, euler #=2 (134598,403788,269192) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.03-->8.95) (max @ vno 72167 --> 135219) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.03-->8.95) (max @ vno 72167 --> 135219) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 144 mutations (34.6%), 272 crossovers (65.4%), 207 vertices were eliminated building final representation... 1378 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=134598, nf=269192, ne=403788, g=0) writing corrected surface to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 21.8 minutes 0 defective edges removing intersecting faces 000: 220 intersecting 001: 2 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 134598 - 403788 + 269192 = 2 --> 0 holes F =2V-4: 269192 = 269196-4 (0) 2E=3F: 807576 = 807576 (0) total defect index = 0 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 58 intersecting 001: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Mon Oct 13 20:01:43 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Andre_v_5_3 rh only generating white matter surface 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->5.20) (max @ vno 72167 --> 134425) face area 0.29 +- 0.12 (0.00-->4.07) mean absolute distance = 0.80 +- 0.97 3680 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=68.8, 224 (222) missing vertices, mean dist 0.5 [0.7 (%22.8)->0.8 (%77.2))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.95 +- 0.27 (0.13-->8.09) (max @ vno 72167 --> 134425) face area 0.29 +- 0.14 (0.00-->4.46) mean absolute distance = 0.36 +- 0.77 2538 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8275596.5, rms=15.56 001: dt: 0.5000, sse=7096488.0, rms=11.793 (0.000%) 002: dt: 0.5000, sse=6724913.0, rms=9.264 (0.000%) 003: dt: 0.5000, sse=6681763.0, rms=7.463 (0.000%) 004: dt: 0.5000, sse=6721869.5, rms=6.256 (0.000%) 005: dt: 0.5000, sse=6856708.5, rms=5.482 (0.000%) 006: dt: 0.5000, sse=7029769.5, rms=5.041 (0.000%) 007: dt: 0.5000, sse=7122842.0, rms=4.763 (0.000%) 008: dt: 0.5000, sse=7213209.0, rms=4.635 (0.000%) 009: dt: 0.5000, sse=7216252.5, rms=4.521 (0.000%) rms = 4.49, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7258658.5, rms=4.488 (0.000%) 011: dt: 0.2500, sse=4436539.0, rms=3.049 (0.000%) 012: dt: 0.2500, sse=3858022.5, rms=2.639 (0.000%) 013: dt: 0.2500, sse=3632238.0, rms=2.506 (0.000%) 014: dt: 0.2500, sse=3535064.5, rms=2.412 (0.000%) 015: dt: 0.2500, sse=3482006.2, rms=2.356 (0.000%) 016: dt: 0.2500, sse=3435388.5, rms=2.298 (0.000%) rms = 2.25, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3410463.5, rms=2.249 (0.000%) 018: dt: 0.1250, sse=3286673.8, rms=2.095 (0.000%) rms = 2.07, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3256495.5, rms=2.069 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=72.1, 101 (62) missing vertices, mean dist -0.2 [0.4 (%68.7)->0.2 (%31.3))] %64 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.09-->8.23) (max @ vno 72167 --> 134425) face area 0.37 +- 0.17 (0.00-->5.92) mean absolute distance = 0.29 +- 0.55 2599 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4000585.2, rms=5.32 020: dt: 0.5000, sse=4457206.5, rms=3.622 (0.000%) rms = 4.10, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=3969262.8, rms=2.561 (0.000%) 022: dt: 0.2500, sse=3744915.0, rms=2.025 (0.000%) 023: dt: 0.2500, sse=3651256.8, rms=1.754 (0.000%) rms = 1.71, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3616158.2, rms=1.707 (0.000%) 025: dt: 0.1250, sse=3527777.0, rms=1.559 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3496436.0, rms=1.537 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=75.0, 96 (48) missing vertices, mean dist -0.2 [0.3 (%67.4)->0.2 (%32.6))] %73 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.10-->8.33) (max @ vno 72167 --> 134425) face area 0.36 +- 0.17 (0.00-->6.02) mean absolute distance = 0.25 +- 0.42 2550 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3869754.0, rms=4.21 027: dt: 0.5000, sse=4387486.5, rms=3.548 (0.000%) rms = 3.93, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3947240.0, rms=2.346 (0.000%) 029: dt: 0.2500, sse=3742988.8, rms=1.861 (0.000%) 030: dt: 0.2500, sse=3724176.2, rms=1.568 (0.000%) rms = 1.56, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=3713214.2, rms=1.558 (0.000%) 032: dt: 0.1250, sse=3637291.2, rms=1.378 (0.000%) rms = 1.36, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3612852.0, rms=1.356 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=76.3, 84 (41) missing vertices, mean dist -0.1 [0.3 (%56.0)->0.2 (%44.0))] %78 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3675275.8, rms=2.21 rms = 2.68, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=3767620.0, rms=1.488 (0.000%) 035: dt: 0.2500, sse=3965457.8, rms=1.082 (0.000%) rms = 1.05, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=4015643.8, rms=1.054 (0.000%) rms = 1.03, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4052535.2, rms=1.034 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 1825 vertices erasing segment 0 (vno[0] = 39876) erasing segment 2 (vno[0] = 84218) erasing segment 3 (vno[0] = 87737) erasing segment 4 (vno[0] = 87751) erasing segment 5 (vno[0] = 87782) erasing segment 6 (vno[0] = 88737) erasing segment 7 (vno[0] = 92380) erasing segment 8 (vno[0] = 92393) erasing segment 9 (vno[0] = 97827) erasing segment 10 (vno[0] = 102984) erasing segment 11 (vno[0] = 104055) erasing segment 12 (vno[0] = 105686) erasing segment 13 (vno[0] = 106494) erasing segment 14 (vno[0] = 109809) erasing segment 15 (vno[0] = 112374) erasing segment 16 (vno[0] = 112995) erasing segment 17 (vno[0] = 113686) erasing segment 18 (vno[0] = 113697) writing cortex label to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.cortex.label... writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.curv writing smoothed area to rh.area writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.area vertex spacing 0.92 +- 0.26 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.36 +- 0.17 (0.00-->6.01) refinement took 5.4 minutes #-------------------------------------------- #@# Smooth2 rh Mon Oct 13 20:07:05 CEST 2014 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts 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 rh Mon Oct 13 20:07:08 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.3 mm, total surface area = 87781 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.111 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.017 (target=0.015) step 060: RMS=0.017 (target=0.015) inflation complete. inflation took 0.5 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 171 vertices thresholded to be in k1 ~ [-1.15 0.34], k2 ~ [-0.13 0.19] total integrated curvature = 0.546*4pi (6.865) --> 0 handles ICI = 1.4, FI = 8.7, variation=150.189 118 vertices thresholded to be in [-0.03 0.03] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 111 vertices thresholded to be in [-0.37 0.14] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.021 done. #----------------------------------------- #@# Curvature Stats rh Mon Oct 13 20:08:54 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 255 ] Gb_filter = 0 WARN: S lookup min: -0.384488 WARN: S explicit min: 0.000000 vertex = 1125 #-------------------------------------------- #@# Sphere rh Mon Oct 13 20:08:58 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, 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 %19.82 pass 1: epoch 2 of 3 starting distance error %19.77 unfolding complete - removing small folds... starting distance error %19.67 removing remaining folds... final distance error %19.69 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.74 hours #-------------------------------------------- #@# Surf Reg rh Mon Oct 13 20:53:33 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.612 curvature mean = 0.032, std = 0.933 curvature mean = 0.009, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 392863.9, tmin=0.8979 d=32.00 min @ (8.00, 8.00, 8.00) sse = 299372.4, tmin=1.8017 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 281465.4, tmin=2.7174 d=8.00 min @ (2.00, 2.00, 2.00) sse = 272550.2, tmin=3.6550 d=2.00 min @ (0.00, -0.50, -0.50) sse = 271783.1, tmin=5.5537 d=1.00 min @ (0.25, 0.00, 0.00) sse = 271765.7, tmin=6.4958 d=0.50 min @ (0.00, 0.12, 0.12) sse = 271743.5, tmin=7.4398 tol=1.0e+00, sigma=0.5, host=psyk-, 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 7.44 min curvature mean = 0.004, std = 0.935 curvature mean = 0.003, std = 0.945 curvature mean = -0.002, std = 0.944 curvature mean = 0.002, std = 0.975 curvature mean = -0.003, std = 0.945 curvature mean = 0.000, std = 0.988 2 Reading smoothwm curvature mean = -0.020, std = 0.291 curvature mean = 0.007, std = 0.069 curvature mean = 0.037, std = 0.332 curvature mean = 0.007, std = 0.083 curvature mean = 0.024, std = 0.500 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.622 curvature mean = 0.007, std = 0.092 curvature mean = 0.004, std = 0.723 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Mon Oct 13 21:17:00 CEST 2014 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Mon Oct 13 21:17:01 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Mon Oct 13 21:17:03 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1442 labels changed using aseg relabeling using gibbs priors... 000: 2951 changed, 134598 examined... 001: 644 changed, 12684 examined... 002: 162 changed, 3674 examined... 003: 52 changed, 950 examined... 004: 20 changed, 328 examined... 005: 5 changed, 116 examined... 006: 4 changed, 38 examined... 007: 3 changed, 25 examined... 008: 2 changed, 19 examined... 009: 3 changed, 12 examined... 010: 0 changed, 11 examined... 167 labels changed using aseg 000: 110 total segments, 71 labels (288 vertices) changed 001: 40 total segments, 1 labels (7 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1282 vertices marked for relabeling... 1282 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 48 seconds. #-------------------------------------------- #@# Make Pial Surf rh Mon Oct 13 21:17:51 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->5.20) (max @ vno 72167 --> 134425) face area 0.29 +- 0.12 (0.00-->4.07) mean absolute distance = 0.81 +- 0.98 3159 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 212 points - only 18.40% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 372 points - only 9.41% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 10 with 80 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=68.9, 225 (223) missing vertices, mean dist 0.5 [0.7 (%22.9)->0.8 (%77.1))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.95 +- 0.27 (0.13-->8.09) (max @ vno 72167 --> 134425) face area 0.29 +- 0.14 (0.00-->4.46) mean absolute distance = 0.36 +- 0.77 2612 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8313815.0, rms=15.55 001: dt: 0.5000, sse=7146796.0, rms=11.809 (0.000%) 002: dt: 0.5000, sse=6781295.0, rms=9.310 (0.000%) 003: dt: 0.5000, sse=6751818.0, rms=7.551 (0.000%) 004: dt: 0.5000, sse=6797656.0, rms=6.386 (0.000%) 005: dt: 0.5000, sse=6938629.0, rms=5.638 (0.000%) 006: dt: 0.5000, sse=7114581.0, rms=5.212 (0.000%) 007: dt: 0.5000, sse=7213681.5, rms=4.944 (0.000%) 008: dt: 0.5000, sse=7301671.0, rms=4.821 (0.000%) 009: dt: 0.5000, sse=7308899.0, rms=4.706 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7345646.0, rms=4.662 (0.000%) 011: dt: 0.2500, sse=4507853.0, rms=3.296 (0.000%) 012: dt: 0.2500, sse=3927899.2, rms=2.913 (0.000%) 013: dt: 0.2500, sse=3700164.5, rms=2.782 (0.000%) 014: dt: 0.2500, sse=3602761.5, rms=2.690 (0.000%) 015: dt: 0.2500, sse=3544500.2, rms=2.627 (0.000%) 016: dt: 0.2500, sse=3497563.5, rms=2.577 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3469812.2, rms=2.535 (0.000%) 018: dt: 0.1250, sse=3345961.2, rms=2.397 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3315012.5, rms=2.370 (0.000%) positioning took 1.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 316 points - only 27.53% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 342 points - only 10.23% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=72.1, 208 (76) missing vertices, mean dist -0.2 [0.4 (%68.6)->0.2 (%31.4))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.37 +- 0.17 (0.00-->5.95) mean absolute distance = 0.30 +- 0.56 2604 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063785.0, rms=5.40 020: dt: 0.5000, sse=4523467.0, rms=3.735 (0.000%) rms = 4.19, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4032946.2, rms=2.720 (0.000%) 022: dt: 0.2500, sse=3805957.8, rms=2.206 (0.000%) 023: dt: 0.2500, sse=3707945.8, rms=1.936 (0.000%) 024: dt: 0.2500, sse=3668042.2, rms=1.867 (0.000%) 025: dt: 0.2500, sse=3630981.5, rms=1.789 (0.000%) rms = 1.76, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3622747.5, rms=1.758 (0.000%) 027: dt: 0.1250, sse=3544567.0, rms=1.642 (0.000%) rms = 1.63, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3519431.2, rms=1.626 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 273 points - only 21.98% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 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 25 points - only 0.00% unknown deleting segment 6 with 355 points - only 9.86% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=75.0, 213 (40) missing vertices, mean dist -0.2 [0.3 (%67.2)->0.2 (%32.8))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.36 +- 0.17 (0.00-->5.94) mean absolute distance = 0.25 +- 0.43 2596 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3888091.5, rms=4.21 029: dt: 0.5000, sse=4422753.5, rms=3.553 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3978346.2, rms=2.353 (0.000%) 031: dt: 0.2500, sse=3775159.0, rms=1.874 (0.000%) 032: dt: 0.2500, sse=3753626.8, rms=1.587 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3742703.0, rms=1.581 (0.000%) 034: dt: 0.1250, sse=3663753.8, rms=1.402 (0.000%) rms = 1.38, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3635901.0, rms=1.375 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 260 points - only 22.31% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown deleting segment 6 with 360 points - only 9.72% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=76.2, 214 (38) missing vertices, mean dist -0.1 [0.3 (%55.9)->0.2 (%44.1))] %78 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3697700.8, rms=2.20 rms = 2.68, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3792608.8, rms=1.495 (0.000%) 037: dt: 0.2500, sse=3992508.8, rms=1.111 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4045497.2, rms=1.083 (0.000%) rms = 1.06, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4078604.5, rms=1.058 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 40.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=44.6, 185 (185) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %14 local maxima, %68 large gradients and %12 min vals, 1135 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27757564.0, rms=31.51 001: dt: 0.5000, sse=19622334.0, rms=25.962 (0.000%) 002: dt: 0.5000, sse=13969531.0, rms=21.285 (0.000%) 003: dt: 0.5000, sse=10452963.0, rms=17.595 (0.000%) 004: dt: 0.5000, sse=8683913.0, rms=14.616 (0.000%) 005: dt: 0.5000, sse=7454407.0, rms=12.132 (0.000%) 006: dt: 0.5000, sse=6748061.5, rms=10.122 (0.000%) 007: dt: 0.5000, sse=6216010.0, rms=8.495 (0.000%) 008: dt: 0.5000, sse=6009703.5, rms=7.175 (0.000%) 009: dt: 0.5000, sse=5901022.5, rms=6.182 (0.000%) 010: dt: 0.5000, sse=5902673.5, rms=5.458 (0.000%) 011: dt: 0.5000, sse=5943038.5, rms=5.003 (0.000%) 012: dt: 0.5000, sse=6007918.0, rms=4.693 (0.000%) 013: dt: 0.5000, sse=6031596.5, rms=4.489 (0.000%) 014: dt: 0.5000, sse=6078880.0, rms=4.313 (0.000%) 015: dt: 0.5000, sse=6087874.5, rms=4.205 (0.000%) 016: dt: 0.5000, sse=6121907.5, rms=4.086 (0.000%) 017: dt: 0.5000, sse=6107810.0, rms=4.026 (0.000%) 018: dt: 0.5000, sse=6112403.5, rms=3.951 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6106326.0, rms=3.924 (0.000%) 020: dt: 0.2500, sse=4101950.2, rms=3.083 (0.000%) 021: dt: 0.2500, sse=3851306.8, rms=2.892 (0.000%) 022: dt: 0.2500, sse=3748330.0, rms=2.840 (0.000%) rms = 2.82, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3727270.0, rms=2.817 (0.000%) 024: dt: 0.1250, sse=3592225.0, rms=2.731 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3571643.8, rms=2.722 (0.000%) positioning took 2.2 minutes mean border=42.3, 540 (30) missing vertices, mean dist 0.3 [0.2 (%52.3)->0.8 (%47.7))] %35 local maxima, %50 large gradients and % 9 min vals, 343 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4304544.5, rms=5.31 026: dt: 0.5000, sse=4590206.5, rms=4.247 (0.000%) 027: dt: 0.5000, sse=5616884.0, rms=4.038 (0.000%) 028: dt: 0.5000, sse=5905539.0, rms=3.948 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4744676.5, rms=3.233 (0.000%) 030: dt: 0.2500, sse=4440080.5, rms=2.929 (0.000%) 031: dt: 0.2500, sse=4299986.0, rms=2.827 (0.000%) rms = 2.78, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4288588.5, rms=2.785 (0.000%) 033: dt: 0.1250, sse=4163390.2, rms=2.700 (0.000%) rms = 2.69, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4147538.2, rms=2.686 (0.000%) positioning took 0.8 minutes mean border=39.8, 695 (21) missing vertices, mean dist 0.2 [0.2 (%42.0)->0.6 (%58.0))] %52 local maxima, %33 large gradients and % 8 min vals, 423 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4533188.5, rms=4.56 035: dt: 0.5000, sse=4724519.5, rms=3.730 (0.000%) rms = 3.71, time step reduction 1 of 3 to 0.250... 036: dt: 0.5000, sse=5770925.0, rms=3.710 (0.000%) 037: dt: 0.2500, sse=4644892.5, rms=2.853 (0.000%) 038: dt: 0.2500, sse=4592182.5, rms=2.656 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4505625.5, rms=2.621 (0.000%) 040: dt: 0.1250, sse=4391475.5, rms=2.515 (0.000%) rms = 2.50, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4382284.5, rms=2.500 (0.000%) positioning took 0.6 minutes mean border=38.2, 1473 (10) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.4 (%55.9))] %63 local maxima, %23 large gradients and % 8 min vals, 454 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4500635.0, rms=3.25 rms = 3.37, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=4368730.5, rms=2.816 (0.000%) 043: dt: 0.2500, sse=4366523.5, rms=2.539 (0.000%) 044: dt: 0.2500, sse=4431401.0, rms=2.440 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=4462294.5, rms=2.395 (0.000%) 046: dt: 0.1250, sse=4389830.0, rms=2.342 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=4388312.0, rms=2.324 (0.000%) positioning took 0.6 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.area.pial vertex spacing 1.04 +- 0.43 (0.03-->8.77) (max @ vno 101298 --> 101320) face area 0.43 +- 0.32 (0.00-->9.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed thickness calculation complete, 593:1166 truncations. 43529 vertices at 0 distance 101643 vertices at 1 distance 75487 vertices at 2 distance 24049 vertices at 3 distance 6180 vertices at 4 distance 1804 vertices at 5 distance 613 vertices at 6 distance 225 vertices at 7 distance 93 vertices at 8 distance 44 vertices at 9 distance 37 vertices at 10 distance 18 vertices at 11 distance 23 vertices at 12 distance 15 vertices at 13 distance 20 vertices at 14 distance 12 vertices at 15 distance 5 vertices at 16 distance 0 vertices at 17 distance 3 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.thickness positioning took 10.8 minutes #-------------------------------------------- #@# Surf Volume rh Mon Oct 13 21:28:41 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Mon Oct 13 21:28:42 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts pctsurfcon --s Andre_v_5_3 --rh-only Log file is /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts/pctsurfcon.log Mon Oct 13 21:28:42 CEST 2014 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts /usr/local/freesurfer/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux psyk-stud141.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_vol2surf --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.wm.mgh --regheader Andre_v_5_3 --cortex srcvol = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz as target reference. Loading label /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.cortex.label Reading surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 = 81204 Masking with /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.cortex.label Writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.wm.mgh Dim: 134598 1 1 mri_vol2surf --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.gm.mgh --projfrac 0.3 --regheader Andre_v_5_3 --cortex srcvol = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz as target reference. Loading label /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.cortex.label Reading surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Done reading source surface Reading thickness /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 = 91544 Masking with /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.cortex.label Writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.gm.mgh Dim: 134598 1 1 mri_concat /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.wm.mgh /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/tmp.pctsurfcon.54230/rh.gm.mgh --paired-diff-norm --mul 100 --o /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.w-g.pct.mgh mri_segstats --in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.w-g.pct.mgh --annot Andre_v_5_3 rh aparc --sum /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.w-g.pct.mgh --annot Andre_v_5_3 rh aparc --sum /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/stats/rh.w-g.pct.stats --snr sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.w-g.pct.mgh Vertex Area is 0.708202 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1232 894.315 2 2002 caudalanteriorcingulate 1116 800.395 3 2003 caudalmiddlefrontal 3207 2245.638 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2049 1463.919 6 2006 entorhinal 404 316.150 7 2007 fusiform 5123 3652.801 8 2008 inferiorparietal 6629 4801.330 9 2009 inferiortemporal 4891 3666.076 10 2010 isthmuscingulate 1622 1110.149 11 2011 lateraloccipital 8145 5802.097 12 2012 lateralorbitofrontal 3592 2646.562 13 2013 lingual 4440 3199.294 14 2014 medialorbitofrontal 2062 1609.531 15 2015 middletemporal 4993 3791.127 16 2016 parahippocampal 945 681.184 17 2017 paracentral 2576 1725.433 18 2018 parsopercularis 1780 1228.908 19 2019 parsorbitalis 999 730.065 20 2020 parstriangularis 2088 1522.350 21 2021 pericalcarine 1722 1237.530 22 2022 postcentral 6804 4611.376 23 2023 posteriorcingulate 1957 1411.572 24 2024 precentral 7273 4837.815 25 2025 precuneus 6016 4152.085 26 2026 rostralanteriorcingulate 1006 690.021 27 2027 rostralmiddlefrontal 7968 5946.072 28 2028 superiorfrontal 10622 7613.397 29 2029 superiorparietal 8026 5717.405 30 2030 superiortemporal 5467 3936.459 31 2031 supramarginal 5160 3622.302 32 2032 frontalpole 500 378.220 33 2033 temporalpole 629 499.348 34 2034 transversetemporal 627 428.204 35 2035 insula 3085 2145.830 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Mon Oct 13 21:28:49 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Andre_v_5_3 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/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 1232 894 2069 2.210 0.518 0.087 0.015 5 0.8 bankssts 1116 800 2165 2.419 0.763 0.129 0.025 14 1.1 caudalanteriorcingulate 3207 2246 5563 2.146 0.558 0.129 0.080 74 5.2 caudalmiddlefrontal 2049 1464 2813 1.732 0.387 0.157 0.042 28 3.7 cuneus 404 316 1765 3.996 0.738 0.117 0.043 4 0.5 entorhinal 5123 3653 9817 2.382 0.736 0.142 0.042 72 8.7 fusiform 6629 4801 11074 2.054 0.535 0.134 0.039 87 10.5 inferiorparietal 4891 3666 10089 2.283 0.750 0.153 0.070 160 11.5 inferiortemporal 1622 1110 3022 2.552 0.856 0.136 0.052 22 3.1 isthmuscingulate 8145 5802 11500 1.802 0.555 0.141 0.036 95 11.8 lateraloccipital 3592 2647 6233 2.086 0.692 0.142 0.044 46 6.3 lateralorbitofrontal 4440 3199 7321 2.103 0.714 0.155 0.054 75 9.3 lingual 2062 1610 3891 2.086 0.888 0.154 0.047 37 3.9 medialorbitofrontal 4993 3791 11489 2.436 0.689 0.145 0.052 84 9.5 middletemporal 945 681 2140 2.687 0.842 0.102 0.024 7 0.9 parahippocampal 2576 1725 3557 1.913 0.568 0.105 0.022 20 2.4 paracentral 1780 1229 3548 2.384 0.599 0.121 0.034 19 2.3 parsopercularis 999 730 1920 1.916 0.660 0.155 0.057 20 2.3 parsorbitalis 2088 1522 3827 2.152 0.540 0.130 0.043 30 3.2 parstriangularis 1722 1238 1813 1.527 0.426 0.148 0.048 24 3.1 pericalcarine 6804 4611 8559 1.702 0.557 0.118 0.031 71 8.6 postcentral 1957 1412 3394 2.135 0.703 0.148 0.049 30 3.9 posteriorcingulate 7273 4838 11327 2.089 0.652 0.103 0.022 53 6.9 precentral 6016 4152 9562 2.157 0.710 0.129 0.043 224 11.7 precuneus 1006 690 2291 2.811 0.884 0.151 0.065 20 2.4 rostralanteriorcingulate 7968 5946 13200 1.849 0.628 0.166 0.082 196 28.2 rostralmiddlefrontal 10622 7613 19720 2.213 0.679 0.127 0.036 119 16.3 superiorfrontal 8026 5717 11581 1.847 0.532 0.129 0.030 89 9.5 superiorparietal 5467 3936 11269 2.483 0.661 0.128 0.031 64 7.3 superiortemporal 5160 3622 9329 2.301 0.544 0.129 0.038 64 7.7 supramarginal 500 378 1064 2.138 0.579 0.211 0.092 15 1.9 frontalpole 629 499 2546 3.521 0.773 0.155 0.050 12 1.1 temporalpole 627 428 889 1.831 0.546 0.121 0.031 5 0.7 transversetemporal 3085 2146 6792 2.955 1.036 0.119 0.040 37 4.4 insula #----------------------------------------- #@# Cortical Parc 2 rh Mon Oct 13 21:29:02 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 35 labels changed using aseg relabeling using gibbs priors... 000: 9376 changed, 134598 examined... 001: 2217 changed, 35957 examined... 002: 671 changed, 11377 examined... 003: 279 changed, 3718 examined... 004: 125 changed, 1525 examined... 005: 65 changed, 746 examined... 006: 25 changed, 351 examined... 007: 13 changed, 143 examined... 008: 7 changed, 64 examined... 009: 5 changed, 37 examined... 010: 6 changed, 35 examined... 011: 7 changed, 37 examined... 012: 5 changed, 34 examined... 013: 6 changed, 32 examined... 014: 4 changed, 30 examined... 015: 6 changed, 27 examined... 016: 2 changed, 26 examined... 017: 0 changed, 8 examined... 14 labels changed using aseg 000: 300 total segments, 216 labels (2485 vertices) changed 001: 96 total segments, 12 labels (136 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 110 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 686 vertices marked for relabeling... 686 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 54 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Mon Oct 13 21:29:56 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -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 Andre_v_5_3 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.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 1085 821 1977 1.942 0.623 0.182 0.068 24 3.0 G_and_S_frontomargin 1660 1163 2965 2.150 0.667 0.133 0.034 19 2.3 G_and_S_occipital_inf 1470 957 2004 1.795 0.615 0.116 0.025 15 1.6 G_and_S_paracentral 1501 1060 2753 2.370 0.511 0.143 0.046 20 2.9 G_and_S_subcentral 1150 883 2493 2.099 0.618 0.218 0.108 56 5.3 G_and_S_transv_frontopol 2578 1849 4964 2.274 0.916 0.143 0.051 43 4.9 G_and_S_cingul-Ant 1612 1155 2773 2.220 0.574 0.109 0.021 12 1.4 G_and_S_cingul-Mid-Ant 1354 976 2428 2.193 0.610 0.125 0.030 13 1.7 G_and_S_cingul-Mid-Post 593 446 1500 2.644 0.609 0.198 0.066 13 1.6 G_cingul-Post-dorsal 295 204 859 3.425 0.806 0.152 0.058 5 0.6 G_cingul-Post-ventral 1880 1349 2580 1.692 0.383 0.161 0.047 26 3.6 G_cuneus 1098 793 2982 2.771 0.489 0.135 0.043 17 1.7 G_front_inf-Opercular 386 278 886 2.450 0.520 0.166 0.076 11 0.8 G_front_inf-Orbital 822 629 1984 2.414 0.579 0.151 0.051 14 1.6 G_front_inf-Triangul 3895 2945 8248 2.207 0.652 0.177 0.133 142 18.7 G_front_middle 7080 5091 14743 2.302 0.714 0.134 0.040 98 12.4 G_front_sup 433 338 1176 3.228 0.986 0.103 0.036 3 0.3 G_Ins_lg_and_S_cent_ins 665 460 2200 3.529 0.929 0.169 0.077 19 2.0 G_insular_short 2066 1508 3581 2.009 0.519 0.158 0.051 34 4.2 G_occipital_middle 2214 1612 3389 1.760 0.483 0.145 0.037 29 3.2 G_occipital_sup 1748 1246 4114 2.659 0.670 0.149 0.048 34 3.3 G_oc-temp_lat-fusifor 2839 2065 5193 2.211 0.767 0.163 0.053 45 5.8 G_oc-temp_med-Lingual 1326 990 4010 3.122 1.083 0.122 0.046 14 2.2 G_oc-temp_med-Parahip 2476 1915 5559 2.294 0.774 0.175 0.070 55 6.9 G_orbital 2577 2003 5637 2.236 0.567 0.165 0.060 52 5.8 G_pariet_inf-Angular 2272 1634 5153 2.538 0.509 0.150 0.049 40 4.4 G_pariet_inf-Supramar 2422 1777 4142 1.919 0.539 0.133 0.034 32 3.3 G_parietal_sup 2527 1744 3474 1.682 0.464 0.134 0.034 35 3.5 G_postcentral 2612 1723 5274 2.407 0.605 0.111 0.027 21 2.8 G_precentral 2632 1889 5058 2.216 0.712 0.152 0.045 43 4.9 G_precuneus 544 509 1424 2.226 0.730 0.210 0.059 13 1.4 G_rectus 352 233 717 2.842 1.029 0.093 0.036 4 0.5 G_subcallosal 516 363 804 1.854 0.582 0.129 0.032 5 0.6 G_temp_sup-G_T_transv 1935 1478 5172 2.676 0.654 0.159 0.047 33 4.0 G_temp_sup-Lateral 649 481 1868 3.274 0.758 0.096 0.021 4 0.5 G_temp_sup-Plan_polar 766 531 1276 2.161 0.427 0.111 0.024 6 0.7 G_temp_sup-Plan_tempo 2616 2015 6311 2.385 0.774 0.173 0.094 133 8.0 G_temporal_inf 3049 2396 8447 2.599 0.638 0.161 0.061 64 6.5 G_temporal_middle 528 368 715 1.951 0.341 0.098 0.020 3 0.5 Lat_Fis-ant-Horizont 232 155 283 1.980 0.410 0.106 0.021 1 0.2 Lat_Fis-ant-Vertical 1728 1162 2414 2.371 0.561 0.114 0.029 13 2.0 Lat_Fis-post 3643 2654 4659 1.626 0.444 0.148 0.042 45 5.9 Pole_occipital 1480 1243 5115 2.814 0.877 0.192 0.082 38 4.6 Pole_temporal 2080 1459 2515 1.867 0.804 0.161 0.084 196 8.2 S_calcarine 3151 2066 2988 1.518 0.486 0.089 0.019 13 2.6 S_central 1668 1171 2310 1.921 0.591 0.098 0.020 11 1.4 S_cingul-Marginalis 698 467 1180 2.507 0.687 0.113 0.027 5 0.8 S_circular_insula_ant 1138 777 1634 2.320 0.908 0.079 0.013 5 0.7 S_circular_insula_inf 1352 917 1716 2.112 0.476 0.104 0.023 7 1.3 S_circular_insula_sup 1103 804 1951 2.253 0.954 0.111 0.026 10 1.1 S_collat_transv_ant 844 581 1111 1.911 0.406 0.142 0.035 12 1.1 S_collat_transv_post 1866 1295 2520 1.835 0.464 0.141 0.053 29 3.3 S_front_inf 2025 1526 2550 1.509 0.501 0.142 0.049 26 3.6 S_front_middle 2823 1969 3735 1.898 0.499 0.107 0.024 19 2.7 S_front_sup 327 206 370 1.708 0.380 0.093 0.013 2 0.2 S_interm_prim-Jensen 3098 2101 3978 1.996 0.538 0.120 0.027 28 3.3 S_intrapariet_and_P_trans 1125 786 1136 1.574 0.430 0.127 0.027 9 1.3 S_oc_middle_and_Lunatus 1320 915 1669 1.831 0.523 0.122 0.026 12 1.4 S_oc_sup_and_transversal 554 397 871 2.100 0.362 0.137 0.076 9 1.0 S_occipital_ant 1277 863 1663 2.078 0.571 0.122 0.030 10 1.6 S_oc-temp_lat 2046 1434 3105 2.323 0.623 0.113 0.026 14 2.3 S_oc-temp_med_and_Lingual 325 222 381 1.487 0.391 0.086 0.014 1 0.2 S_orbital_lateral 667 482 875 1.771 0.948 0.091 0.017 3 0.3 S_orbital_med-olfact 1180 833 1607 1.772 0.550 0.136 0.042 13 1.9 S_orbital-H_Shaped 1988 1333 2253 1.870 0.618 0.101 0.020 12 1.7 S_parieto_occipital 1852 1160 1854 2.066 0.848 0.119 0.039 25 2.9 S_pericallosal 2658 1800 3001 1.667 0.488 0.094 0.018 15 2.0 S_postcentral 1614 1102 2176 2.058 0.425 0.102 0.019 9 1.3 S_precentral-inf-part 1368 933 1482 1.692 0.474 0.104 0.020 9 1.1 S_precentral-sup-part 203 151 353 2.195 0.655 0.164 0.049 4 0.4 S_suborbital 1578 1085 2467 2.287 0.431 0.121 0.032 15 1.9 S_subparietal 1442 971 1741 2.062 0.633 0.114 0.026 10 1.5 S_temporal_inf 5730 3974 8149 2.099 0.570 0.102 0.022 43 5.2 S_temporal_sup 349 241 493 2.274 0.458 0.141 0.030 4 0.5 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Mon Oct 13 21:30:10 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1287 labels changed using aseg relabeling using gibbs priors... 000: 2678 changed, 134598 examined... 001: 615 changed, 11531 examined... 002: 180 changed, 3439 examined... 003: 62 changed, 1015 examined... 004: 27 changed, 388 examined... 005: 27 changed, 159 examined... 006: 13 changed, 103 examined... 007: 4 changed, 64 examined... 008: 6 changed, 28 examined... 009: 4 changed, 31 examined... 010: 3 changed, 18 examined... 011: 3 changed, 17 examined... 012: 7 changed, 18 examined... 013: 5 changed, 30 examined... 014: 6 changed, 26 examined... 015: 7 changed, 26 examined... 016: 7 changed, 26 examined... 017: 5 changed, 27 examined... 018: 6 changed, 27 examined... 019: 5 changed, 28 examined... 020: 6 changed, 27 examined... 021: 7 changed, 26 examined... 022: 4 changed, 29 examined... 023: 4 changed, 20 examined... 024: 4 changed, 18 examined... 025: 6 changed, 20 examined... 026: 4 changed, 28 examined... 027: 7 changed, 24 examined... 028: 5 changed, 28 examined... 029: 5 changed, 32 examined... 030: 7 changed, 28 examined... 031: 6 changed, 31 examined... 032: 4 changed, 29 examined... 033: 5 changed, 22 examined... 034: 7 changed, 26 examined... 035: 4 changed, 32 examined... 036: 2 changed, 20 examined... 037: 3 changed, 14 examined... 038: 4 changed, 16 examined... 039: 4 changed, 18 examined... 040: 4 changed, 19 examined... 041: 4 changed, 20 examined... 042: 2 changed, 22 examined... 043: 2 changed, 12 examined... 044: 0 changed, 12 examined... 443 labels changed using aseg 000: 70 total segments, 37 labels (114 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 629 vertices marked for relabeling... 629 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Mon Oct 13 21:30:57 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab Andre_v_5_3 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.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 1135 813 2202 2.419 0.763 0.129 0.025 14 1.2 caudalanteriorcingulate 3334 2333 5801 2.163 0.561 0.130 0.079 76 5.4 caudalmiddlefrontal 2648 1863 3543 1.710 0.391 0.147 0.038 33 4.2 cuneus 457 360 1924 3.944 0.738 0.116 0.043 4 0.5 entorhinal 4613 3255 8731 2.393 0.745 0.138 0.039 63 7.4 fusiform 6242 4532 10382 2.042 0.535 0.136 0.040 82 10.2 inferiorparietal 5361 4023 11038 2.271 0.741 0.154 0.070 168 12.6 inferiortemporal 1592 1087 2970 2.542 0.859 0.136 0.052 22 3.1 isthmuscingulate 8456 6053 12152 1.811 0.560 0.140 0.036 99 12.2 lateraloccipital 3911 2947 7386 2.126 0.752 0.157 0.057 66 8.7 lateralorbitofrontal 4468 3224 7373 2.104 0.712 0.154 0.053 75 9.3 lingual 1709 1356 3534 2.212 0.880 0.168 0.056 36 4.0 medialorbitofrontal 5825 4402 12909 2.405 0.668 0.137 0.047 89 10.1 middletemporal 954 686 2145 2.684 0.840 0.103 0.025 7 0.9 parahippocampal 2656 1777 3720 1.937 0.578 0.106 0.023 21 2.5 paracentral 1843 1274 3563 2.362 0.578 0.120 0.034 20 2.3 parsopercularis 1091 766 1849 1.922 0.667 0.135 0.042 18 1.8 parsorbitalis 2288 1664 4168 2.140 0.567 0.131 0.042 33 3.4 parstriangularis 1738 1252 1832 1.528 0.435 0.150 0.049 26 3.3 pericalcarine 7231 4923 9464 1.736 0.581 0.118 0.030 75 9.0 postcentral 2049 1474 3484 2.128 0.693 0.149 0.049 32 4.0 posteriorcingulate 7028 4649 11056 2.108 0.648 0.104 0.023 52 6.7 precentral 6134 4256 9787 2.153 0.706 0.130 0.043 224 11.9 precuneus 1086 745 2435 2.806 0.869 0.149 0.062 21 2.4 rostralanteriorcingulate 5094 3768 8224 1.835 0.616 0.163 0.089 117 20.4 rostralmiddlefrontal 13534 9832 24464 2.114 0.693 0.135 0.042 193 23.6 superiorfrontal 6794 4828 9800 1.861 0.538 0.130 0.031 77 8.3 superiorparietal 6855 4976 15044 2.556 0.743 0.127 0.032 81 9.1 superiortemporal 4996 3484 8776 2.285 0.535 0.128 0.037 61 7.4 supramarginal 628 429 887 1.829 0.546 0.120 0.031 5 0.7 transversetemporal 3005 2085 6495 2.872 1.032 0.118 0.037 35 4.2 insula #-------------------------------------------- #@# Cortical ribbon mask Mon Oct 13 21:31:10 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon Andre_v_5_3 SUBJECTS_DIR is /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 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 = 24 writing volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Mon Oct 13 21:39:17 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject Andre_v_5_3 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/ASegStatsLUT.txt --subject Andre_v_5_3 sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 atlas_icv (eTIV) = 1836896 mm^3 (det: 1.060542 ) Computing euler number orig.nofix lheno = -20, rheno = -34 orig.nofix lhholes = 11, rhholes = 18 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 216319.859 216749.000 diff= -429.1 pctdiff=-0.198 rhCtxGM: 214575.387 215125.000 diff= -549.6 pctdiff=-0.256 lhCtxWM: 276114.913 276683.000 diff= -568.1 pctdiff=-0.206 rhCtxWM: 280265.098 279540.000 diff= 725.1 pctdiff= 0.259 SubCortGMVol 65060.000 SupraTentVol 1109083.257 (1107983.000) diff=1100.257 pctdiff=0.099 SupraTentVolNotVent 1054578.257 (1053478.000) diff=1100.257 pctdiff=0.104 BrainSegVol 1257550.000 (1253264.000) diff=4286.000 pctdiff=0.341 BrainSegVolNotVent 1197350.000 (1196255.257) diff=1094.743 pctdiff=0.091 BrainSegVolNotVent 1197350.000 CerebellumVol 143599.000 VentChorVol 54505.000 3rd4th5thCSF 5695.000 CSFVol 1453.000, OptChiasmVol 229.000 MaskVol 1833202.000 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 3 4 Left-Lateral-Ventricle 19861 19860.721 4 5 Left-Inf-Lat-Vent 715 714.691 5 7 Left-Cerebellum-White-Matter 15470 15469.986 6 8 Left-Cerebellum-Cortex 56297 56297.445 7 10 Left-Thalamus-Proper 7746 7745.975 8 11 Left-Caudate 3983 3983.185 9 12 Left-Putamen 7822 7822.277 10 13 Left-Pallidum 1687 1686.790 11 14 3rd-Ventricle 2364 2363.830 12 15 4th-Ventricle 2160 2160.025 13 16 Brain-Stem 23484 23484.402 14 17 Left-Hippocampus 4023 4022.562 15 18 Left-Amygdala 1810 1810.399 16 24 CSF 1393 1392.536 17 26 Left-Accumbens-area 886 886.050 18 28 Left-VentralDC 4050 4049.621 19 30 Left-vessel 141 141.327 20 31 Left-choroid-plexus 1647 1646.623 23 43 Right-Lateral-Ventricle 29456 29455.553 24 44 Right-Inf-Lat-Vent 947 947.056 25 46 Right-Cerebellum-White-Matter 15942 15941.921 26 47 Right-Cerebellum-Cortex 58058 58058.066 27 49 Right-Thalamus-Proper 7313 7313.041 28 50 Right-Caudate 4214 4214.087 29 51 Right-Putamen 7295 7295.319 30 52 Right-Pallidum 1626 1625.686 31 53 Right-Hippocampus 3972 3972.230 32 54 Right-Amygdala 2038 2038.430 33 58 Right-Accumbens-area 778 778.128 34 60 Right-VentralDC 4071 4071.088 35 62 Right-vessel 182 182.459 36 63 Right-choroid-plexus 2057 2057.448 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 3750 3750.101 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 35 34.681 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 264 263.607 45 251 CC_Posterior 1097 1097.235 46 252 CC_Mid_Posterior 417 417.104 47 253 CC_Central 474 474.205 48 254 CC_Mid_Anterior 527 526.803 49 255 CC_Anterior 1074 1073.763 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Mon Oct 13 21:41:27 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_aparc2aseg --s Andre_v_5_3 --volmask SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 subject Andre_v_5_3 outvol /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading lh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial Loading lh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading rh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial Loading rh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 428305 Used brute-force search on 0 voxels Writing output aseg to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc+aseg.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_aparc2aseg --s Andre_v_5_3 --volmask --a2009s SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 subject Andre_v_5_3 outvol /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading lh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial Loading lh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading rh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial Loading rh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 428305 Used brute-force search on 0 voxels Writing output aseg to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Mon Oct 13 21:43:41 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_aparc2aseg --s Andre_v_5_3 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 subject Andre_v_5_3 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc+aseg.mgz Reading lh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading lh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial Loading lh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading rh pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial Loading rh annotations from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/ribbon.mgz Loading filled from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9979 vertices from left hemi Ripped 9843 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz Loading Ctx Seg File /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- 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 = 984200 Used brute-force search on 2671 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1.000000 1 k 3.000000 2 k 1.000000 3 k 4.000000 4 k 1747.000000 5 k 3.000000 6 k 2.000000 7 k 1.000000 Fixing Parahip RH WM Found 2 clusters 0 k 4.000000 1 k 1543.000000 Writing output aseg to mri/wmparc.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 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 Andre_v_5_3 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 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 Andre_v_5_3 --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi UseRobust 0 atlas_icv (eTIV) = 1836896 mm^3 (det: 1.060542 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 216319.859 216749.000 diff= -429.1 pctdiff=-0.198 rhCtxGM: 214575.387 215125.000 diff= -549.6 pctdiff=-0.256 lhCtxWM: 276114.913 276683.000 diff= -568.1 pctdiff=-0.206 rhCtxWM: 280265.098 279540.000 diff= 725.1 pctdiff= 0.259 SubCortGMVol 65060.000 SupraTentVol 1109083.257 (1107983.000) diff=1100.257 pctdiff=0.099 SupraTentVolNotVent 1054578.257 (1053478.000) diff=1100.257 pctdiff=0.104 BrainSegVol 1257550.000 (1253264.000) diff=4286.000 pctdiff=0.341 BrainSegVolNotVent 1197350.000 (1196255.257) diff=1094.743 pctdiff=0.091 BrainSegVolNotVent 1197350.000 CerebellumVol 143599.000 VentChorVol 54505.000 3rd4th5thCSF 5695.000 CSFVol 1453.000, OptChiasmVol 229.000 MaskVol 1833202.000 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 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2219 2219.311 2 3002 wm-lh-caudalanteriorcingulate 2990 2990.381 3 3003 wm-lh-caudalmiddlefrontal 8126 8126.393 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 2271 2271.100 6 3006 wm-lh-entorhinal 924 923.594 7 3007 wm-lh-fusiform 7733 7732.969 8 3008 wm-lh-inferiorparietal 10621 10621.259 9 3009 wm-lh-inferiortemporal 7035 7034.632 10 3010 wm-lh-isthmuscingulate 4506 4505.942 11 3011 wm-lh-lateraloccipital 10738 10738.475 12 3012 wm-lh-lateralorbitofrontal 6413 6412.555 13 3013 wm-lh-lingual 6394 6394.312 14 3014 wm-lh-medialorbitofrontal 3730 3729.509 15 3015 wm-lh-middletemporal 6274 6274.173 16 3016 wm-lh-parahippocampal 1849 1848.892 17 3017 wm-lh-paracentral 4206 4205.622 18 3018 wm-lh-parsopercularis 4471 4470.670 19 3019 wm-lh-parsorbitalis 883 882.578 20 3020 wm-lh-parstriangularis 3641 3640.543 21 3021 wm-lh-pericalcarine 3168 3167.932 22 3022 wm-lh-postcentral 9285 9285.238 23 3023 wm-lh-posteriorcingulate 5771 5770.597 24 3024 wm-lh-precentral 15362 15361.729 25 3025 wm-lh-precuneus 10030 10030.193 26 3026 wm-lh-rostralanteriorcingulate 2658 2657.742 27 3027 wm-lh-rostralmiddlefrontal 13234 13234.284 28 3028 wm-lh-superiorfrontal 19701 19700.654 29 3029 wm-lh-superiorparietal 14607 14607.370 30 3030 wm-lh-superiortemporal 9778 9778.051 31 3031 wm-lh-supramarginal 13267 13266.640 32 3032 wm-lh-frontalpole 263 263.224 33 3033 wm-lh-temporalpole 984 983.811 34 3034 wm-lh-transversetemporal 1008 1007.534 35 3035 wm-lh-insula 8178 8178.332 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 3032 3032.293 120 4002 wm-rh-caudalanteriorcingulate 3473 3473.186 121 4003 wm-rh-caudalmiddlefrontal 6433 6432.908 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 2770 2769.652 124 4006 wm-rh-entorhinal 678 678.243 125 4007 wm-rh-fusiform 8900 8900.149 126 4008 wm-rh-inferiorparietal 10933 10933.274 127 4009 wm-rh-inferiortemporal 7773 7773.284 128 4010 wm-rh-isthmuscingulate 4370 4370.223 129 4011 wm-rh-lateraloccipital 13443 13443.233 130 4012 wm-rh-lateralorbitofrontal 7261 7261.040 131 4013 wm-rh-lingual 5979 5979.208 132 4014 wm-rh-medialorbitofrontal 3381 3380.755 133 4015 wm-rh-middletemporal 6752 6752.438 134 4016 wm-rh-parahippocampal 1652 1651.896 135 4017 wm-rh-paracentral 5433 5433.357 136 4018 wm-rh-parsopercularis 3111 3110.510 137 4019 wm-rh-parsorbitalis 1227 1226.874 138 4020 wm-rh-parstriangularis 3646 3645.929 139 4021 wm-rh-pericalcarine 3019 3018.961 140 4022 wm-rh-postcentral 9461 9460.749 141 4023 wm-rh-posteriorcingulate 5118 5117.870 142 4024 wm-rh-precentral 14606 14605.938 143 4025 wm-rh-precuneus 11122 11121.942 144 4026 wm-rh-rostralanteriorcingulate 2549 2548.992 145 4027 wm-rh-rostralmiddlefrontal 14405 14405.227 146 4028 wm-rh-superiorfrontal 21506 21506.160 147 4029 wm-rh-superiorparietal 14064 14063.788 148 4030 wm-rh-superiortemporal 8316 8315.691 149 4031 wm-rh-supramarginal 9521 9520.707 150 4032 wm-rh-frontalpole 483 483.111 151 4033 wm-rh-temporalpole 922 921.849 152 4034 wm-rh-transversetemporal 747 746.911 153 4035 wm-rh-insula 8281 8280.904 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 47402 47401.574 237 5002 Right-UnsegmentedWhiteMatter 50139 50138.859 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label #-------------------------------------------- #@# BA Labels lh Mon Oct 13 21:52:43 CEST 2014 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA1.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 372 Checking for and removing duplicates Writing label file ./lh.BA1.label 4501 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA2.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 813 Checking for and removing duplicates Writing label file ./lh.BA2.label 8722 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3a.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA3a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 130 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4207 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3b.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA3b.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 354 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6337 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4a.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA4a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 342 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6126 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4p.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA4p.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 168 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4238 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA6.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA6.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 1102 Checking for and removing duplicates Writing label file ./lh.BA6.label 14691 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA44.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA44.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 519 Checking for and removing duplicates Writing label file ./lh.BA44.label 4700 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA45.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA45.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 621 Checking for and removing duplicates Writing label file ./lh.BA45.label 4043 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V1.label --trgsubject Andre_v_5_3 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.V1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 881 Checking for and removing duplicates Writing label file ./lh.V1.label 5522 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V2.label --trgsubject Andre_v_5_3 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.V2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 2558 Checking for and removing duplicates Writing label file ./lh.V2.label 10672 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.MT.label --trgsubject Andre_v_5_3 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.MT.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 254 Checking for and removing duplicates Writing label file ./lh.MT.label 2272 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.perirhinal.label --trgsubject Andre_v_5_3 --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.perirhinal.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1296 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA1.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 63 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1077 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA2.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 356 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2448 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3a.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA3a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 23 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1527 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3b.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA3b.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2149 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4a.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA4a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2435 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4p.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA4p.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 58 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1607 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA6.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA6.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 531 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7566 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA44.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA44.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 284 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 2196 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA45.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.BA45.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 268 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1419 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V1.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.V1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 567 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 3972 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V2.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.V2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 1122 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4456 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.MT.thresh.label --trgsubject Andre_v_5_3 --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./lh.MT.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 133935 Number of reverse mapping hits = 30 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 543 mri_label2label: Done mris_label2annot --s Andre_v_5_3 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label cmdline mris_label2annot --s Andre_v_5_3 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi subject Andre_v_5_3 hemi lh SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 93170 unhit vertices Writing annot to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.BA.annot mris_label2annot --s Andre_v_5_3 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label cmdline mris_label2annot --s Andre_v_5_3 --hemi lh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi subject Andre_v_5_3 hemi lh SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 110633 unhit vertices Writing annot to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab Andre_v_5_3 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 1088 739 1480 1.680 0.470 0.150 0.052 17 2.2 BA1 4798 3362 6609 1.807 0.508 0.125 0.033 55 6.7 BA2 897 606 724 1.454 0.348 0.111 0.025 5 0.9 BA3a 2432 1689 2827 1.527 0.582 0.106 0.023 19 2.4 BA3b 1676 1033 2632 2.182 0.677 0.095 0.022 11 1.7 BA4a 1212 771 1574 2.062 0.638 0.085 0.021 4 0.9 BA4p 9483 6593 17002 2.236 0.642 0.119 0.034 94 11.4 BA6 2652 1883 5014 2.292 0.501 0.130 0.036 34 3.7 BA44 2960 2186 5716 2.185 0.591 0.136 0.035 37 4.0 BA45 2909 2139 4004 1.719 0.481 0.154 0.051 41 6.1 V1 8125 5750 11564 1.857 0.588 0.158 0.238 448 138.3 V2 1561 1114 2333 1.899 0.443 0.137 0.037 19 2.3 MT 972 719 3017 3.070 0.965 0.104 0.023 7 0.8 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab Andre_v_5_3 lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 695 445 936 1.741 0.339 0.166 0.063 13 1.7 BA1 2011 1394 2551 1.650 0.415 0.126 0.035 24 2.7 BA2 751 507 583 1.401 0.302 0.113 0.024 4 0.7 BA3a 1558 1056 1377 1.241 0.300 0.095 0.020 10 1.3 BA3b 1604 998 2531 2.200 0.684 0.089 0.040 15 1.3 BA4a 1002 637 1298 2.096 0.663 0.087 0.024 4 0.9 BA4p 5255 3586 9121 2.220 0.633 0.120 0.031 48 6.7 BA6 1712 1197 3340 2.378 0.471 0.136 0.040 26 2.6 BA44 1241 929 2617 2.248 0.517 0.142 0.032 16 1.7 BA45 3155 2332 4308 1.691 0.483 0.154 0.049 44 6.5 V1 3978 2840 5314 1.747 0.492 0.166 0.445 393 131.9 V2 340 255 539 1.858 0.449 0.139 0.043 5 0.5 MT #-------------------------------------------- #@# BA Labels rh Mon Oct 13 21:56:08 CEST 2014 mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA1.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 433 Checking for and removing duplicates Writing label file ./rh.BA1.label 4395 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA2.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 593 Checking for and removing duplicates Writing label file ./rh.BA2.label 7280 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3a.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA3a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 192 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4172 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3b.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA3b.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 392 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4914 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4a.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA4a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 424 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6171 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4p.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA4p.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 180 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4653 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA6.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA6.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 981 Checking for and removing duplicates Writing label file ./rh.BA6.label 13237 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA44.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA44.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 450 Checking for and removing duplicates Writing label file ./rh.BA44.label 7362 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA45.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA45.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 703 Checking for and removing duplicates Writing label file ./rh.BA45.label 6058 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V1.label --trgsubject Andre_v_5_3 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.V1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 1253 Checking for and removing duplicates Writing label file ./rh.V1.label 5980 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V2.label --trgsubject Andre_v_5_3 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.V2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 3457 Checking for and removing duplicates Writing label file ./rh.V2.label 11473 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.MT.label --trgsubject Andre_v_5_3 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.MT.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 383 Checking for and removing duplicates Writing label file ./rh.MT.label 2315 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.perirhinal.label --trgsubject Andre_v_5_3 --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.perirhinal.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 140 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 892 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA1.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 152 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1028 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA2.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 221 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 2909 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3a.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA3a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 53 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1751 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3b.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA3b.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 213 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2396 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4a.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA4a.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1472 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4p.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA4p.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 62 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1551 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA6.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA6.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 482 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7441 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA44.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA44.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 82 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1094 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA45.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.BA45.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 128 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1306 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V1.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.V1.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 666 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 3898 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V2.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.V2.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 1692 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 5129 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.MT.thresh.label --trgsubject Andre_v_5_3 --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = Andre_v_5_3 trglabel = ./rh.MT.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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white Reading target registration /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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 134598 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 294 mri_label2label: Done mris_label2annot --s Andre_v_5_3 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label cmdline mris_label2annot --s Andre_v_5_3 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi subject Andre_v_5_3 hemi rh SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 93513 unhit vertices Writing annot to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.BA.annot mris_label2annot --s Andre_v_5_3 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label cmdline mris_label2annot --s Andre_v_5_3 --hemi rh --ctab /usr/local/freesurfer/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname psyk-stud141.uio.no machine x86_64 user evaghi subject Andre_v_5_3 hemi rh SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 ColorTable /usr/local/freesurfer/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 112030 unhit vertices Writing annot to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab Andre_v_5_3 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 1036 702 1562 1.821 0.442 0.162 0.050 19 2.3 BA1 3528 2434 4545 1.723 0.508 0.099 0.021 25 3.0 BA2 1123 727 903 1.422 0.388 0.110 0.024 7 1.1 BA3a 2276 1542 2455 1.449 0.435 0.112 0.028 23 2.6 BA3b 1517 957 2361 2.135 0.712 0.087 0.017 8 1.1 BA4a 1228 784 1501 1.887 0.635 0.090 0.021 6 1.1 BA4p 8128 5646 13993 2.105 0.666 0.117 0.031 82 11.2 BA6 3248 2274 5941 2.302 0.538 0.121 0.030 32 3.7 BA44 3988 2876 7088 2.050 0.596 0.137 0.049 63 6.9 BA45 3365 2556 4388 1.603 0.448 0.158 0.076 77 8.4 V1 9050 6421 13194 1.889 0.651 0.158 0.058 343 23.0 V2 1894 1320 2755 2.011 0.462 0.124 0.033 19 2.4 MT 704 551 2838 3.505 1.145 0.148 0.078 20 1.8 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab Andre_v_5_3 rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /usr/local/freesurfer/average/colortable_BA.txt) Saving annotation colortable ./BA.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 794 527 1244 1.880 0.403 0.162 0.042 15 1.4 BA1 2035 1409 2590 1.691 0.488 0.096 0.019 13 1.5 BA2 987 628 717 1.387 0.356 0.109 0.024 5 1.0 BA3a 1803 1228 1750 1.357 0.380 0.097 0.022 12 1.6 BA3b 980 590 1378 2.039 0.752 0.095 0.019 12 0.9 BA4a 990 641 1305 2.014 0.688 0.081 0.018 3 0.7 BA4p 5091 3493 8733 2.109 0.686 0.111 0.025 39 5.0 BA6 782 572 1898 2.533 0.612 0.123 0.035 10 1.1 BA44 995 760 2289 2.395 0.595 0.147 0.043 15 1.6 BA45 3175 2410 4026 1.579 0.446 0.157 0.075 75 7.9 V1 4720 3363 6781 1.847 0.652 0.173 0.073 151 14.4 V2 216 155 368 2.015 0.310 0.124 0.039 4 0.2 MT /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Mon Oct 13 21:59:34 CEST 2014 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014; ln -s /usr/local/freesurfer/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o Andre_v_5_3 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject Andre_v_5_3. processing subject lh.EC_average... reading output surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 924 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label Andre_v_5_3 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white... INFO: assuming MGZ format for volumes. 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 316 231 1221 3.360 0.828 0.121 0.044 4 0.7 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Mon Oct 13 21:59:47 CEST 2014 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014; ln -s /usr/local/freesurfer/subjects/rh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o Andre_v_5_3 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject Andre_v_5_3. processing subject rh.EC_average... reading output surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 852 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label Andre_v_5_3 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... reading input surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... reading input pial surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... reading input white surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white... INFO: assuming MGZ format for volumes. 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 334 235 1386 3.283 1.135 0.162 0.085 9 1.2 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Mon Oct 13 13:45:36 CEST 2014 Ended at Mon Oct 13 21:59:59 CEST 2014 #@#%# recon-all-run-time-hours 8.240 recon-all -s Andre_v_5_3 finished without error at Mon Oct 13 21:59:59 CEST 2014 New invocation of recon-all Tue Oct 14 10:55:30 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 /usr/local/freesurfer/bin/recon-all -autorecon3 -s Andre_v_5_3 -FLAIR test_output_Andre/FLAIR/flair.nii -FLAIRpial subjid Andre_v_5_3 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 49416388 23677884 25738504 15520 279372 20990620 -/+ buffers/cache: 2407892 47008496 Swap: 10485756 0 10485756 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-08:55:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Tue Oct 14 10:55:33 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_convert --no_scale 1 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz... #----------------------------------------- #@# Curvature Stats lh Tue Oct 14 10:55:34 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.327954 WARN: S explicit min: 0.000000 vertex = 144 #-------------------------------------------- #@# Sphere lh Tue Oct 14 10:55:38 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.53 pass 1: epoch 2 of 3 starting distance error %19.55 unfolding complete - removing small folds... starting distance error %19.46 removing remaining folds... final distance error %19.48 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.73 hours #-------------------------------------------- #@# Surf Reg lh Tue Oct 14 11:39:38 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.602 curvature mean = 0.041, std = 0.932 curvature mean = 0.008, std = 0.869 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 307117.9, tmin=0.8050 d=32.00 min @ (0.00, 8.00, 0.00) sse = 226073.8, tmin=1.6187 d=16.00 min @ (0.00, 0.00, 4.00) sse = 211214.2, tmin=2.4359 d=4.00 min @ (1.00, 0.00, -1.00) sse = 210319.8, tmin=4.0929 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 209823.5, tmin=4.9321 d=1.00 min @ (0.00, 0.25, 0.25) sse = 209721.6, tmin=5.7708 d=0.50 min @ (0.00, 0.00, -0.12) sse = 209715.5, tmin=6.6282 tol=1.0e+00, sigma=0.5, host=psyk-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.63 min curvature mean = 0.022, std = 0.950 curvature mean = 0.004, std = 0.946 curvature mean = 0.019, std = 0.961 curvature mean = 0.002, std = 0.976 curvature mean = 0.018, std = 0.964 curvature mean = 0.000, std = 0.990 2 Reading smoothwm curvature mean = -0.019, std = 0.253 curvature mean = 0.005, std = 0.067 curvature mean = 0.043, std = 0.380 curvature mean = 0.005, std = 0.079 curvature mean = 0.027, std = 0.580 curvature mean = 0.005, std = 0.086 curvature mean = 0.015, std = 0.719 curvature mean = 0.005, std = 0.088 curvature mean = 0.005, std = 0.823 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 1113: 33 negative triangles #-------------------------------------------- #@# Jacobian white lh Tue Oct 14 12:08:40 CEST 2014 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Oct 14 12:08:42 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Oct 14 12:08:43 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1458 labels changed using aseg relabeling using gibbs priors... 000: 2902 changed, 133935 examined... 001: 673 changed, 12460 examined... 002: 171 changed, 3779 examined... 003: 43 changed, 1038 examined... 004: 15 changed, 278 examined... 005: 6 changed, 101 examined... 006: 0 changed, 40 examined... 255 labels changed using aseg 000: 108 total segments, 67 labels (266 vertices) changed 001: 43 total segments, 4 labels (12 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 847 vertices marked for relabeling... 847 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 46 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Oct 14 12:09:29 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.06-->3.71) (max @ vno 100459 --> 106413) face area 0.29 +- 0.12 (0.00-->1.27) mean absolute distance = 0.79 +- 0.96 3792 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 130 points - only 14.62% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 831 points - only 0.00% unknown deleting segment 5 with 45 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown deleting segment 7 with 40 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 49 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown mean border=69.0, 141 (141) missing vertices, mean dist 0.5 [0.7 (%22.6)->0.8 (%77.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.94 +- 0.27 (0.10-->3.15) (max @ vno 69317 --> 69300) face area 0.29 +- 0.14 (0.00-->1.64) mean absolute distance = 0.34 +- 0.72 2450 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7931433.0, rms=15.08 001: dt: 0.5000, sse=6935160.0, rms=11.406 (0.000%) 002: dt: 0.5000, sse=6544342.5, rms=8.907 (0.000%) 003: dt: 0.5000, sse=6586972.0, rms=7.155 (0.000%) 004: dt: 0.5000, sse=6627329.5, rms=5.998 (0.000%) 005: dt: 0.5000, sse=6865879.0, rms=5.255 (0.000%) 006: dt: 0.5000, sse=6919816.5, rms=4.836 (0.000%) 007: dt: 0.5000, sse=7114851.5, rms=4.565 (0.000%) 008: dt: 0.5000, sse=7097618.5, rms=4.438 (0.000%) 009: dt: 0.5000, sse=7203923.0, rms=4.325 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7126259.0, rms=4.290 (0.000%) 011: dt: 0.2500, sse=4362082.0, rms=2.797 (0.000%) 012: dt: 0.2500, sse=3801983.2, rms=2.360 (0.000%) 013: dt: 0.2500, sse=3582298.0, rms=2.212 (0.000%) 014: dt: 0.2500, sse=3481731.8, rms=2.118 (0.000%) 015: dt: 0.2500, sse=3421952.2, rms=2.059 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3381572.5, rms=2.015 (0.000%) 017: dt: 0.1250, sse=3263632.2, rms=1.881 (0.000%) rms = 1.86, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3235483.2, rms=1.861 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 161 points - only 17.39% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 4 with 645 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 20 points - only 0.00% unknown deleting segment 9 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown deleting segment 13 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 16 with 61 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown mean border=72.2, 79 (46) missing vertices, mean dist -0.2 [0.4 (%70.0)->0.3 (%30.0))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.12-->3.28) (max @ vno 93103 --> 92209) face area 0.37 +- 0.17 (0.00-->1.96) mean absolute distance = 0.29 +- 0.53 2944 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3970987.0, rms=5.17 019: dt: 0.5000, sse=4454506.0, rms=3.513 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3973708.8, rms=2.475 (0.000%) 021: dt: 0.2500, sse=3767152.8, rms=1.990 (0.000%) 022: dt: 0.2500, sse=3656728.5, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3623260.8, rms=1.686 (0.000%) 024: dt: 0.1250, sse=3536692.2, rms=1.560 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3505861.5, rms=1.540 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 168 points - only 16.67% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 686 points - only 0.00% unknown deleting segment 4 with 40 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 57 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown mean border=75.1, 77 (43) missing vertices, mean dist -0.2 [0.3 (%68.3)->0.2 (%31.7))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.13-->3.56) (max @ vno 111457 --> 111456) face area 0.36 +- 0.16 (0.00-->2.01) mean absolute distance = 0.25 +- 0.41 2338 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3865593.2, rms=4.13 026: dt: 0.5000, sse=4328042.5, rms=3.538 (0.000%) rms = 3.87, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3907882.5, rms=2.334 (0.000%) 028: dt: 0.2500, sse=3723624.5, rms=1.850 (0.000%) 029: dt: 0.2500, sse=3709880.0, rms=1.549 (0.000%) rms = 1.55, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3699352.5, rms=1.545 (0.000%) 031: dt: 0.1250, sse=3626586.0, rms=1.384 (0.000%) rms = 1.36, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3604916.5, rms=1.365 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 175 points - only 16.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 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 712 points - only 0.00% unknown deleting segment 5 with 44 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 60 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown mean border=76.3, 81 (39) missing vertices, mean dist -0.1 [0.3 (%56.8)->0.2 (%43.2))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3669868.8, rms=2.21 rms = 2.63, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3762752.2, rms=1.531 (0.000%) 034: dt: 0.2500, sse=3948763.2, rms=1.104 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=3999052.2, rms=1.059 (0.000%) rms = 1.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4031869.2, rms=1.039 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 25.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=44.7, 108 (108) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.0 (%100.0))] %14 local maxima, %66 large gradients and %15 min vals, 1713 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27774222.0, rms=31.55 001: dt: 0.5000, sse=19744250.0, rms=26.075 (0.000%) 002: dt: 0.5000, sse=14127545.0, rms=21.462 (0.000%) 003: dt: 0.5000, sse=10548771.0, rms=17.785 (0.000%) 004: dt: 0.5000, sse=8627045.0, rms=14.803 (0.000%) 005: dt: 0.5000, sse=7348371.5, rms=12.299 (0.000%) 006: dt: 0.5000, sse=6612727.0, rms=10.273 (0.000%) 007: dt: 0.5000, sse=6053383.0, rms=8.576 (0.000%) 008: dt: 0.5000, sse=5788639.0, rms=7.187 (0.000%) 009: dt: 0.5000, sse=5610497.5, rms=6.077 (0.000%) 010: dt: 0.5000, sse=5643526.5, rms=5.275 (0.000%) 011: dt: 0.5000, sse=5587664.0, rms=4.732 (0.000%) 012: dt: 0.5000, sse=5703336.0, rms=4.397 (0.000%) 013: dt: 0.5000, sse=5683819.0, rms=4.153 (0.000%) 014: dt: 0.5000, sse=5771044.0, rms=3.999 (0.000%) 015: dt: 0.5000, sse=5726464.5, rms=3.881 (0.000%) 016: dt: 0.5000, sse=5811575.0, rms=3.800 (0.000%) 017: dt: 0.5000, sse=5761283.5, rms=3.730 (0.000%) 018: dt: 0.5000, sse=5797567.0, rms=3.675 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5756588.5, rms=3.635 (0.000%) 020: dt: 0.2500, sse=3891133.2, rms=2.857 (0.000%) 021: dt: 0.2500, sse=3675003.8, rms=2.687 (0.000%) rms = 2.64, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3579567.8, rms=2.641 (0.000%) 023: dt: 0.1250, sse=3450344.5, rms=2.556 (0.000%) rms = 2.55, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3435661.8, rms=2.546 (0.000%) positioning took 2.0 minutes mean border=42.7, 472 (28) missing vertices, mean dist 0.2 [0.2 (%54.3)->0.8 (%45.7))] %33 local maxima, %51 large gradients and %11 min vals, 605 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4060163.5, rms=4.82 025: dt: 0.5000, sse=4331332.5, rms=3.821 (0.000%) 026: dt: 0.5000, sse=5401962.0, rms=3.678 (0.000%) 027: dt: 0.5000, sse=5601610.0, rms=3.578 (0.000%) rms = 3.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4500867.0, rms=2.911 (0.000%) 029: dt: 0.2500, sse=4218836.0, rms=2.637 (0.000%) 030: dt: 0.2500, sse=4089517.2, rms=2.547 (0.000%) rms = 2.51, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4061397.5, rms=2.515 (0.000%) 032: dt: 0.1250, sse=3957642.5, rms=2.438 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3947623.5, rms=2.426 (0.000%) positioning took 0.8 minutes mean border=40.4, 678 (23) missing vertices, mean dist 0.2 [0.2 (%43.4)->0.5 (%56.6))] %51 local maxima, %33 large gradients and %10 min vals, 678 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4268281.0, rms=4.13 034: dt: 0.5000, sse=4423501.5, rms=3.341 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4168684.0, rms=2.780 (0.000%) 036: dt: 0.2500, sse=4205171.5, rms=2.458 (0.000%) 037: dt: 0.2500, sse=4173098.5, rms=2.378 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4184372.2, rms=2.341 (0.000%) 039: dt: 0.1250, sse=4097827.0, rms=2.291 (0.000%) rms = 2.28, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4094593.8, rms=2.283 (0.000%) positioning took 0.6 minutes mean border=38.8, 1433 (17) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %61 local maxima, %22 large gradients and %10 min vals, 636 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4201795.5, rms=3.02 rms = 3.05, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4079617.0, rms=2.582 (0.000%) 042: dt: 0.2500, sse=4110240.2, rms=2.267 (0.000%) 043: dt: 0.2500, sse=4164422.8, rms=2.161 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4187721.8, rms=2.118 (0.000%) rms = 2.07, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4126205.8, rms=2.073 (0.000%) positioning took 0.5 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area.pial vertex spacing 1.03 +- 0.42 (0.08-->7.11) (max @ vno 99529 --> 98590) face area 0.43 +- 0.31 (0.00-->8.42) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed thickness calculation complete, 568:1039 truncations. 39591 vertices at 0 distance 100082 vertices at 1 distance 77896 vertices at 2 distance 25453 vertices at 3 distance 6940 vertices at 4 distance 2124 vertices at 5 distance 713 vertices at 6 distance 268 vertices at 7 distance 106 vertices at 8 distance 52 vertices at 9 distance 45 vertices at 10 distance 28 vertices at 11 distance 18 vertices at 12 distance 16 vertices at 13 distance 7 vertices at 14 distance 12 vertices at 15 distance 6 vertices at 16 distance 2 vertices at 17 distance 7 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.thickness positioning took 10.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue Oct 14 12:19:35 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Curvature Stats rh Tue Oct 14 12:19:36 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 255 ] Gb_filter = 0 WARN: S lookup min: -0.384488 WARN: S explicit min: 0.000000 vertex = 1125 #-------------------------------------------- #@# Sphere rh Tue Oct 14 12:19:40 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, 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 %19.82 pass 1: epoch 2 of 3 starting distance error %19.77 unfolding complete - removing small folds... starting distance error %19.67 removing remaining folds... final distance error %19.69 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.70 hours #-------------------------------------------- #@# Surf Reg rh Tue Oct 14 13:01:26 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.612 curvature mean = 0.032, std = 0.933 curvature mean = 0.009, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 392863.9, tmin=0.8204 d=32.00 min @ (8.00, 8.00, 8.00) sse = 299372.4, tmin=1.6433 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 281465.4, tmin=2.4784 d=8.00 min @ (2.00, 2.00, 2.00) sse = 272550.2, tmin=3.3371 d=2.00 min @ (0.00, -0.50, -0.50) sse = 271783.1, tmin=5.0918 d=1.00 min @ (0.25, 0.00, 0.00) sse = 271765.7, tmin=5.9546 d=0.50 min @ (0.00, 0.12, 0.12) sse = 271743.5, tmin=6.8211 tol=1.0e+00, sigma=0.5, host=psyk-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.82 min curvature mean = 0.004, std = 0.935 curvature mean = 0.003, std = 0.945 curvature mean = -0.002, std = 0.944 curvature mean = 0.002, std = 0.975 curvature mean = -0.003, std = 0.945 curvature mean = 0.000, std = 0.988 2 Reading smoothwm curvature mean = -0.020, std = 0.291 curvature mean = 0.007, std = 0.069 curvature mean = 0.037, std = 0.332 curvature mean = 0.007, std = 0.083 curvature mean = 0.024, std = 0.500 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.622 curvature mean = 0.007, std = 0.092 curvature mean = 0.004, std = 0.723 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Oct 14 13:22:25 CEST 2014 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Oct 14 13:22:26 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Oct 14 13:22:28 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1442 labels changed using aseg relabeling using gibbs priors... 000: 2951 changed, 134598 examined... 001: 644 changed, 12684 examined... 002: 162 changed, 3674 examined... 003: 52 changed, 950 examined... 004: 20 changed, 328 examined... 005: 5 changed, 116 examined... 006: 4 changed, 38 examined... 007: 3 changed, 25 examined... 008: 2 changed, 19 examined... 009: 3 changed, 12 examined... 010: 0 changed, 11 examined... 167 labels changed using aseg 000: 110 total segments, 71 labels (288 vertices) changed 001: 40 total segments, 1 labels (7 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1282 vertices marked for relabeling... 1282 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 47 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Oct 14 13:23:15 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->5.20) (max @ vno 72167 --> 134425) face area 0.29 +- 0.12 (0.00-->4.07) mean absolute distance = 0.81 +- 0.98 3159 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 212 points - only 18.40% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 372 points - only 9.41% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 10 with 80 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=68.9, 225 (223) missing vertices, mean dist 0.5 [0.7 (%22.9)->0.8 (%77.1))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.95 +- 0.27 (0.13-->8.09) (max @ vno 72167 --> 134425) face area 0.29 +- 0.14 (0.00-->4.46) mean absolute distance = 0.36 +- 0.77 2612 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8313815.0, rms=15.55 001: dt: 0.5000, sse=7146796.0, rms=11.809 (0.000%) 002: dt: 0.5000, sse=6781295.0, rms=9.310 (0.000%) 003: dt: 0.5000, sse=6751818.0, rms=7.551 (0.000%) 004: dt: 0.5000, sse=6797656.0, rms=6.386 (0.000%) 005: dt: 0.5000, sse=6938629.0, rms=5.638 (0.000%) 006: dt: 0.5000, sse=7114581.0, rms=5.212 (0.000%) 007: dt: 0.5000, sse=7213681.5, rms=4.944 (0.000%) 008: dt: 0.5000, sse=7301671.0, rms=4.821 (0.000%) 009: dt: 0.5000, sse=7308899.0, rms=4.706 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7345646.0, rms=4.662 (0.000%) 011: dt: 0.2500, sse=4507853.0, rms=3.296 (0.000%) 012: dt: 0.2500, sse=3927899.2, rms=2.913 (0.000%) 013: dt: 0.2500, sse=3700164.5, rms=2.782 (0.000%) 014: dt: 0.2500, sse=3602761.5, rms=2.690 (0.000%) 015: dt: 0.2500, sse=3544500.2, rms=2.627 (0.000%) 016: dt: 0.2500, sse=3497563.5, rms=2.577 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3469812.2, rms=2.535 (0.000%) 018: dt: 0.1250, sse=3345961.2, rms=2.397 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3315012.5, rms=2.370 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 316 points - only 27.53% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 342 points - only 10.23% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=72.1, 208 (76) missing vertices, mean dist -0.2 [0.4 (%68.6)->0.2 (%31.4))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.37 +- 0.17 (0.00-->5.95) mean absolute distance = 0.30 +- 0.56 2604 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063785.0, rms=5.40 020: dt: 0.5000, sse=4523467.0, rms=3.735 (0.000%) rms = 4.19, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4032946.2, rms=2.720 (0.000%) 022: dt: 0.2500, sse=3805957.8, rms=2.206 (0.000%) 023: dt: 0.2500, sse=3707945.8, rms=1.936 (0.000%) 024: dt: 0.2500, sse=3668042.2, rms=1.867 (0.000%) 025: dt: 0.2500, sse=3630981.5, rms=1.789 (0.000%) rms = 1.76, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3622747.5, rms=1.758 (0.000%) 027: dt: 0.1250, sse=3544567.0, rms=1.642 (0.000%) rms = 1.63, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3519431.2, rms=1.626 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 273 points - only 21.98% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 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 25 points - only 0.00% unknown deleting segment 6 with 355 points - only 9.86% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=75.0, 213 (40) missing vertices, mean dist -0.2 [0.3 (%67.2)->0.2 (%32.8))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.36 +- 0.17 (0.00-->5.94) mean absolute distance = 0.25 +- 0.43 2596 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3888091.5, rms=4.21 029: dt: 0.5000, sse=4422753.5, rms=3.553 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3978346.2, rms=2.353 (0.000%) 031: dt: 0.2500, sse=3775159.0, rms=1.874 (0.000%) 032: dt: 0.2500, sse=3753626.8, rms=1.587 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3742703.0, rms=1.581 (0.000%) 034: dt: 0.1250, sse=3663753.8, rms=1.402 (0.000%) rms = 1.38, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3635901.0, rms=1.375 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 260 points - only 22.31% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown deleting segment 6 with 360 points - only 9.72% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=76.2, 214 (38) missing vertices, mean dist -0.1 [0.3 (%55.9)->0.2 (%44.1))] %78 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3697700.8, rms=2.20 rms = 2.68, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3792608.8, rms=1.495 (0.000%) 037: dt: 0.2500, sse=3992508.8, rms=1.111 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4045497.2, rms=1.083 (0.000%) rms = 1.06, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4078604.5, rms=1.058 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 40.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=44.6, 185 (185) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %14 local maxima, %68 large gradients and %12 min vals, 1135 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27757564.0, rms=31.51 001: dt: 0.5000, sse=19622334.0, rms=25.962 (0.000%) 002: dt: 0.5000, sse=13969531.0, rms=21.285 (0.000%) 003: dt: 0.5000, sse=10452963.0, rms=17.595 (0.000%) 004: dt: 0.5000, sse=8683913.0, rms=14.616 (0.000%) 005: dt: 0.5000, sse=7454407.0, rms=12.132 (0.000%) 006: dt: 0.5000, sse=6748061.5, rms=10.122 (0.000%) 007: dt: 0.5000, sse=6216010.0, rms=8.495 (0.000%) 008: dt: 0.5000, sse=6009703.5, rms=7.175 (0.000%) 009: dt: 0.5000, sse=5901022.5, rms=6.182 (0.000%) 010: dt: 0.5000, sse=5902673.5, rms=5.458 (0.000%) 011: dt: 0.5000, sse=5943038.5, rms=5.003 (0.000%) 012: dt: 0.5000, sse=6007918.0, rms=4.693 (0.000%) 013: dt: 0.5000, sse=6031596.5, rms=4.489 (0.000%) 014: dt: 0.5000, sse=6078880.0, rms=4.313 (0.000%) 015: dt: 0.5000, sse=6087874.5, rms=4.205 (0.000%) 016: dt: 0.5000, sse=6121907.5, rms=4.086 (0.000%) 017: dt: 0.5000, sse=6107810.0, rms=4.026 (0.000%) 018: dt: 0.5000, sse=6112403.5, rms=3.951 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6106326.0, rms=3.924 (0.000%) 020: dt: 0.2500, sse=4101950.2, rms=3.083 (0.000%) 021: dt: 0.2500, sse=3851306.8, rms=2.892 (0.000%) 022: dt: 0.2500, sse=3748330.0, rms=2.840 (0.000%) rms = 2.82, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3727270.0, rms=2.817 (0.000%) 024: dt: 0.1250, sse=3592225.0, rms=2.731 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3571643.8, rms=2.722 (0.000%) positioning took 2.1 minutes mean border=42.3, 540 (30) missing vertices, mean dist 0.3 [0.2 (%52.3)->0.8 (%47.7))] %35 local maxima, %50 large gradients and % 9 min vals, 343 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4304544.5, rms=5.31 026: dt: 0.5000, sse=4590206.5, rms=4.247 (0.000%) 027: dt: 0.5000, sse=5616884.0, rms=4.038 (0.000%) 028: dt: 0.5000, sse=5905539.0, rms=3.948 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4744676.5, rms=3.233 (0.000%) 030: dt: 0.2500, sse=4440080.5, rms=2.929 (0.000%) 031: dt: 0.2500, sse=4299986.0, rms=2.827 (0.000%) rms = 2.78, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4288588.5, rms=2.785 (0.000%) 033: dt: 0.1250, sse=4163390.2, rms=2.700 (0.000%) rms = 2.69, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4147538.2, rms=2.686 (0.000%) positioning took 0.8 minutes mean border=39.8, 695 (21) missing vertices, mean dist 0.2 [0.2 (%42.0)->0.6 (%58.0))] %52 local maxima, %33 large gradients and % 8 min vals, 423 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4533188.5, rms=4.56 035: dt: 0.5000, sse=4724519.5, rms=3.730 (0.000%) rms = 3.71, time step reduction 1 of 3 to 0.250... 036: dt: 0.5000, sse=5770925.0, rms=3.710 (0.000%) 037: dt: 0.2500, sse=4644892.5, rms=2.853 (0.000%) 038: dt: 0.2500, sse=4592182.5, rms=2.656 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4505625.5, rms=2.621 (0.000%) 040: dt: 0.1250, sse=4391475.5, rms=2.515 (0.000%) rms = 2.50, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4382284.5, rms=2.500 (0.000%) positioning took 0.6 minutes mean border=38.2, 1473 (10) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.4 (%55.9))] %63 local maxima, %23 large gradients and % 8 min vals, 454 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4500635.0, rms=3.25 rms = 3.37, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=4368730.5, rms=2.816 (0.000%) 043: dt: 0.2500, sse=4366523.5, rms=2.539 (0.000%) 044: dt: 0.2500, sse=4431401.0, rms=2.440 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=4462294.5, rms=2.395 (0.000%) 046: dt: 0.1250, sse=4389830.0, rms=2.342 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=4388312.0, rms=2.324 (0.000%) positioning took 0.6 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.area.pial vertex spacing 1.04 +- 0.43 (0.03-->8.77) (max @ vno 101298 --> 101320) face area 0.43 +- 0.32 (0.00-->9.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed thickness calculation complete, 593:1166 truncations. 43529 vertices at 0 distance 101643 vertices at 1 distance 75487 vertices at 2 distance 24049 vertices at 3 distance 6180 vertices at 4 distance 1804 vertices at 5 distance 613 vertices at 6 distance 225 vertices at 7 distance 93 vertices at 8 distance 44 vertices at 9 distance 37 vertices at 10 distance 18 vertices at 11 distance 23 vertices at 12 distance 15 vertices at 13 distance 20 vertices at 14 distance 12 vertices at 15 distance 5 vertices at 16 distance 0 vertices at 17 distance 3 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.thickness positioning took 10.6 minutes #-------------------------------------------- #@# Surf Volume rh Tue Oct 14 13:33:48 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Oct 14 13:33:49 CEST 2014 bbregister --s Andre_v_5_3 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz --lta /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta --init-fsl --T2 Log file is /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat.log Tue Oct 14 13:33:49 CEST 2014 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts /usr/local/freesurfer/bin/bbregister --s Andre_v_5_3 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz --lta /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii... fslregister --s Andre_v_5_3 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister --dof 6 --fsvol brainmask.mgz Log file is /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat.fslregister.log Tue Oct 14 13:33:49 CEST 2014 --s Andre_v_5_3 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ psyk-stud140.uio.no Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brainmask.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/refvol.fslregister.nii mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brainmask.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 3.72529e-08, -8.3819e-08) j_ras = (6.14673e-08, -5.52391e-08, -1) k_ras = (2.2538e-07, 1, 1.83936e-08) writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/refvol.fslregister.nii... -------------------------------------- /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii --frame 0 mri_convert /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344517, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) keeping frame 0 writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii... Mov determinant is -0.95354 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts tkregister2_cmdl --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/reg0.49693.dat --regheader --fslregout /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat.fsl.mat0 --s Andre_v_5_3 --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii reg file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/reg0.49693.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.977 0.000 0.000 125.000; 0.000 0.000 1.000 -6.499; 0.000 -0.977 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.034 0.950 0.309 -0.019; 0.999 -0.029 -0.021 40.987; -0.011 0.309 -0.951 0.002; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.034 0.950 0.309 -0.019; 0.999 -0.029 -0.021 40.987; -0.011 0.309 -0.951 0.002; 0.000 0.000 0.000 1.000; Determinant 1 subject = Andre_v_5_3 RegMat --------------------------- 0.034 0.950 0.309 -0.019; 0.999 -0.029 -0.021 40.987; -0.011 0.309 -0.951 0.002; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.95354, ref det = -1 Tue Oct 14 13:33:52 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts flirt.fsl -ref /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/refvol.fslregister.nii -in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat.fsl.mat0 Tue Oct 14 13:34:02 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts flirt.fsl -ref /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/refvol.fslregister.nii -in /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat.fsl.mat -init /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s Andre_v_5_3 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --fslreg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.036 -0.015 -0.999 171.502; 0.308 -0.951 0.025 207.746; -0.951 -0.309 -0.029 287.100; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii reg file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii Tmov: -------------------- -0.977 0.000 0.000 125.000; 0.000 0.000 1.000 -6.499; 0.000 -0.977 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -0.95354, ref det = -1 ---- Input registration matrix (computed) -------- 0.036 0.951 0.308 -0.116; 0.999 -0.029 -0.025 39.652; -0.015 0.309 -0.951 -0.622; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.036 0.951 0.308 -0.116; 0.999 -0.029 -0.025 39.652; -0.015 0.309 -0.951 -0.622; 0.000 0.000 0.000 1.000; Determinant 1 subject = Andre_v_5_3 RegMat --------------------------- 0.036 0.951 0.308 -0.116; 0.999 -0.029 -0.025 39.652; -0.015 0.309 -0.951 -0.622; 0.000 0.000 0.000 1.000; (standard_in) 1: syntax error Started at Tue Oct 14 13:33:49 CEST 2014 Ended at Tue Oct 14 13:34:12 CEST 2014 fslregister Done To check results, run: tkregister2 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --surf orig mri_segreg --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --init-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --out-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_segreg --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --init-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat --out-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname psyk-stud140.uio.no machine x86_64 user evaghi movvol /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii regfile /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.init.dat subject Andre_v_5_3 dof 6 outregfile /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1413311250 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.036 0.951 0.308 -0.116; 0.999 -0.029 -0.025 39.652; -0.015 0.309 -0.951 -0.622; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.960794 1 -25.0 -25.0 25.0 1.119773 2 -25.0 25.0 -25.0 1.032938 3 -25.0 25.0 25.0 1.039304 4 25.0 -25.0 -25.0 0.985941 5 25.0 -25.0 25.0 1.050647 6 25.0 25.0 -25.0 1.202326 7 25.0 25.0 25.0 0.929154 REL: 8 0.533523 8.320877 1.040110 rel = 0.512949 Initial costs ---------------- Number of surface hits 303 WM Intensity 1151.2887 +/- 294.0555 Ctx Intensity 1298.5697 +/- 303.3997 Pct Contrast 11.6286 +/- 35.7274 Cost 0.5335 RelCost 0.5129 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9975 0.9975 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9294 0.9294 0.0 28 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.0000 0.8734 0.8734 0.0 90 -4.0000 0.0000 -4.0000 0.0000 -4.0000 -4.0000 0.8421 0.8421 0.0 188 -4.0000 4.0000 -4.0000 4.0000 4.0000 4.0000 0.8211 0.8211 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7683 0.7683 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7477 0.7477 0.0 291 0.0000 -4.0000 0.0000 4.0000 0.0000 -4.0000 0.7268 0.7268 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.7131 0.7131 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5335 0.5335 0.0 Brute Force -------------------------- Min cost was 0.533523 Number of iterations 729 Search time 0.893000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 7 -0.067 0.000 0.000 0.000 0.000 0.000 0.5319981394 9 -0.061 0.000 0.000 0.000 0.000 0.000 0.5319242020 11 -0.051 0.000 0.000 0.000 0.000 0.000 0.5318572795 12 -0.050 0.000 0.000 0.000 0.000 0.000 0.5318556337 19 -0.050 0.382 0.000 0.000 0.000 0.000 0.5010839527 23 -0.050 0.354 0.000 0.000 0.000 0.000 0.4972642982 29 -0.050 0.353 0.000 0.000 0.000 0.000 0.4972541843 38 -0.050 0.353 -0.062 0.000 0.000 0.000 0.4949021517 40 -0.050 0.353 -0.090 0.000 0.000 0.000 0.4943540361 41 -0.050 0.353 -0.098 0.000 0.000 0.000 0.4942892187 43 -0.050 0.353 -0.102 0.000 0.000 0.000 0.4942821669 45 -0.050 0.353 -0.101 0.000 0.000 0.000 0.4942817652 61 -0.050 0.353 -0.101 -0.003 0.000 0.000 0.4941569310 62 -0.050 0.353 -0.101 -0.005 0.000 0.000 0.4940810274 63 -0.050 0.353 -0.101 -0.006 0.000 0.000 0.4940329938 70 -0.050 0.353 -0.101 -0.006 0.020 0.000 0.4936708532 72 -0.050 0.353 -0.101 -0.006 0.024 0.000 0.4936578133 95 -0.068 0.353 -0.101 -0.006 0.024 0.000 0.4935848336 96 -0.060 0.353 -0.101 -0.006 0.024 0.000 0.4935721373 97 -0.063 0.353 -0.101 -0.006 0.024 0.000 0.4935702506 98 -0.062 0.353 -0.101 -0.006 0.024 0.000 0.4935696142 120 -0.062 0.353 -0.117 -0.006 0.024 0.000 0.4930973258 122 -0.062 0.353 -0.150 -0.006 0.024 0.000 0.4925467028 124 -0.062 0.353 -0.154 -0.006 0.024 0.000 0.4925294705 125 -0.062 0.353 -0.155 -0.006 0.024 0.000 0.4925266362 138 -0.062 0.353 -0.155 -0.026 0.024 0.000 0.4917099978 139 -0.062 0.353 -0.155 -0.039 0.024 0.000 0.4916279960 140 -0.062 0.353 -0.155 -0.036 0.024 0.000 0.4916076017 141 -0.062 0.353 -0.155 -0.035 0.024 0.000 0.4916049760 149 -0.062 0.353 -0.155 -0.035 0.044 0.000 0.4908432076 150 -0.062 0.353 -0.155 -0.035 0.088 0.000 0.4900773878 151 -0.062 0.353 -0.155 -0.035 0.093 0.000 0.4900470549 152 -0.062 0.353 -0.155 -0.035 0.103 0.000 0.4900055220 154 -0.062 0.353 -0.155 -0.035 0.116 0.000 0.4899954707 155 -0.062 0.353 -0.155 -0.035 0.112 0.000 0.4899916741 157 -0.062 0.353 -0.155 -0.035 0.113 0.000 0.4899915085 170 -0.062 0.353 -0.155 -0.035 0.113 -0.006 0.4895683824 183 -0.080 0.353 -0.155 -0.035 0.113 -0.006 0.4894016526 189 -0.083 0.353 -0.155 -0.035 0.113 -0.006 0.4893767200 190 -0.085 0.353 -0.155 -0.035 0.113 -0.006 0.4893743006 203 -0.085 0.347 -0.155 -0.035 0.113 -0.006 0.4884902238 213 -0.085 0.347 -0.156 -0.035 0.113 -0.006 0.4883822165 216 -0.085 0.347 -0.181 -0.035 0.113 -0.006 0.4863585094 218 -0.085 0.347 -0.194 -0.035 0.113 -0.006 0.4858874735 221 -0.085 0.347 -0.195 -0.035 0.113 -0.006 0.4858721239 252 -0.085 0.347 -0.195 -0.035 0.115 -0.006 0.4858641335 304 -0.085 0.347 -0.193 -0.035 0.115 -0.006 0.4858598141 306 -0.085 0.347 -0.194 -0.035 0.115 -0.006 0.4858390462 335 -0.085 0.347 -0.194 -0.035 0.117 -0.006 0.4858078106 353 -0.085 0.347 -0.193 -0.035 0.119 -0.006 0.4858060402 359 -0.085 0.347 -0.193 -0.035 0.118 -0.006 0.4858048291 371 -0.085 0.347 -0.193 -0.035 0.118 -0.006 0.4858047978 384 -0.086 0.347 -0.193 -0.035 0.118 -0.006 0.4858021423 454 -0.086 0.347 -0.193 -0.035 0.118 -0.006 0.4858019969 460 -0.086 0.347 -0.193 -0.035 0.118 -0.006 0.4858018957 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.953673 1 -25.0 -25.0 25.0 1.129901 2 -25.0 25.0 -25.0 1.066434 3 -25.0 25.0 25.0 1.067664 4 25.0 -25.0 -25.0 0.935009 5 25.0 -25.0 25.0 1.019257 6 25.0 25.0 -25.0 1.165749 7 25.0 25.0 25.0 0.934748 REL: 8 0.485802 8.272435 1.034054 rel = 0.469803 Number of iterations 4 Min cost was 0.485802 Number of FunctionCalls 462 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.568000 sec Parameters at optimum (transmm) -0.08626 0.34686 -0.19324 Parameters at optimum (rotdeg) -0.03474 0.11793 -0.00551 Final costs ---------------- Number of surface hits 299 WM Intensity 1152.0569 +/- 293.7867 Ctx Intensity 1289.1688 +/- 313.8294 Pct Contrast 10.4547 +/- 35.0881 Cost 0.4858 RelCost 0.5129 Reg at min cost was 0.036 0.951 0.306 -0.200; 0.999 -0.029 -0.026 39.998; -0.016 0.307 -0.952 -0.839; 0.000 0.000 0.000 1.000; Writing optimal reg to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat, type = 14 Original Reg 0.036 0.951 0.308 -0.116; 0.999 -0.029 -0.025 39.652; -0.015 0.309 -0.951 -0.622; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.002 0.084; 0.000 -0.000 0.001 -0.346; 0.001 0.002 0.001 0.217; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.406698 Computing change in rh position Surface RMS Diff (mm) 0.412748 0.518347 mri_segreg done mri_segreg --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --init-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat --out-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 cd /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mri_segreg --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii --init-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat --out-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat.mincost --dof 6 --nmax 36 --param /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat.param --surf white --cur-reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname psyk-stud140.uio.no machine x86_64 user evaghi movvol /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/template.nii regfile /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/tmp.bbregister.49657/bbr.pass1.dat subject Andre_v_5_3 dof 6 outregfile /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1414217250 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.036 0.951 0.306 -0.200; 0.999 -0.029 -0.026 39.998; -0.016 0.307 -0.952 -0.839; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.025692 1 -25.0 -25.0 25.0 1.009164 2 -25.0 25.0 -25.0 1.016885 3 -25.0 25.0 25.0 1.002791 4 25.0 -25.0 -25.0 0.974053 5 25.0 -25.0 25.0 1.034338 6 25.0 25.0 -25.0 1.037860 7 25.0 25.0 25.0 0.945152 REL: 8 0.570734 8.045936 1.005742 rel = 0.567475 Initial costs ---------------- Number of surface hits 27800 WM Intensity 1154.1782 +/- 284.2966 Ctx Intensity 1281.1295 +/- 300.8543 Pct Contrast 10.1879 +/- 35.8051 Cost 0.5707 RelCost 0.5675 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5390 0.5390 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.5306 0.5306 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.5285 0.5285 0.0 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.5214 0.5214 0.0 19 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.0000 0.5196 0.5196 0.0 27 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 -0.1000 0.5190 0.5190 0.0 36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.5157 0.5157 0.0 45 -0.1000 -0.1000 0.0000 0.1000 -0.1000 -0.1000 0.5042 0.5042 0.0 46 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0000 0.5026 0.5026 0.0 73 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.0000 0.5016 0.5016 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.4932 0.4932 0.0 291 0.0000 -0.1000 0.0000 0.1000 0.0000 -0.1000 0.4926 0.4926 0.0 315 0.0000 -0.1000 0.1000 0.1000 -0.1000 -0.1000 0.4922 0.4922 0.0 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.4913 0.4913 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4858 0.4858 0.0 Brute Force -------------------------- Min cost was 0.485802 Number of iterations 729 Search time 0.894000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 6 0.382 0.000 0.000 0.000 0.000 0.000 0.5623856786 7 0.342 0.000 0.000 0.000 0.000 0.000 0.5620040788 9 0.329 0.000 0.000 0.000 0.000 0.000 0.5619770591 10 0.328 0.000 0.000 0.000 0.000 0.000 0.5619745566 12 0.325 0.000 0.000 0.000 0.000 0.000 0.5619714658 19 0.325 -0.618 0.000 0.000 0.000 0.000 0.5582373592 21 0.325 -0.390 0.000 0.000 0.000 0.000 0.5507404683 22 0.325 -0.339 0.000 0.000 0.000 0.000 0.5495385606 24 0.325 -0.307 0.000 0.000 0.000 0.000 0.5490716837 26 0.325 -0.289 0.000 0.000 0.000 0.000 0.5488523780 28 0.325 -0.291 0.000 0.000 0.000 0.000 0.5487807525 32 0.325 -0.290 0.000 0.000 0.000 0.000 0.5487472406 34 0.325 -0.290 1.000 0.000 0.000 0.000 0.5482651126 38 0.325 -0.290 0.618 0.000 0.000 0.000 0.5327192939 39 0.325 -0.290 0.429 0.000 0.000 0.000 0.5314935424 40 0.325 -0.290 0.469 0.000 0.000 0.000 0.5314388338 44 0.325 -0.290 0.479 0.000 0.000 0.000 0.5314100346 45 0.325 -0.290 0.480 0.000 0.000 0.000 0.5314080991 54 0.325 -0.290 0.480 0.022 0.000 0.000 0.5309973077 55 0.325 -0.290 0.480 0.181 0.000 0.000 0.5289620889 61 0.325 -0.290 0.480 0.178 0.000 0.000 0.5289486180 73 0.325 -0.290 0.480 0.178 0.009 0.000 0.5289250227 74 0.325 -0.290 0.480 0.178 0.008 0.000 0.5289235292 88 0.325 -0.290 0.480 0.178 0.008 -0.002 0.5288896856 101 0.338 -0.290 0.480 0.178 0.008 -0.002 0.5288083536 103 0.339 -0.290 0.480 0.178 0.008 -0.002 0.5288079891 125 0.339 -0.290 0.498 0.178 0.008 -0.002 0.5287743711 127 0.339 -0.290 0.494 0.178 0.008 -0.002 0.5287702334 151 0.339 -0.290 0.494 0.178 0.027 -0.002 0.5287468046 152 0.339 -0.290 0.494 0.178 0.024 -0.002 0.5287348397 153 0.339 -0.290 0.494 0.178 0.020 -0.002 0.5287302023 174 0.353 -0.290 0.509 0.178 0.032 -0.002 0.5286920659 180 0.347 -0.290 0.503 0.178 0.027 -0.002 0.5286856839 181 0.348 -0.290 0.504 0.178 0.027 -0.002 0.5286852836 182 0.349 -0.290 0.505 0.178 0.029 -0.002 0.5286841457 186 0.349 -0.290 0.505 0.178 0.028 -0.002 0.5286840772 203 0.349 -0.290 0.505 0.178 0.028 -0.000 0.5286665484 220 0.349 -0.291 0.505 0.178 0.028 -0.000 0.5286081180 229 0.349 -0.291 0.501 0.178 0.028 -0.000 0.5286034002 230 0.349 -0.291 0.502 0.178 0.028 -0.000 0.5286031077 254 0.349 -0.291 0.502 0.178 0.027 -0.000 0.5286024573 261 0.354 -0.291 0.507 0.178 0.031 -0.000 0.5286003869 262 0.352 -0.291 0.505 0.178 0.029 -0.000 0.5285961075 265 0.352 -0.291 0.505 0.178 0.029 -0.000 0.5285960978 266 0.352 -0.291 0.505 0.178 0.029 -0.000 0.5285960717 267 0.352 -0.291 0.505 0.178 0.029 -0.000 0.5285959326 311 0.352 -0.291 0.502 0.178 0.029 -0.000 0.5285931395 344 0.353 -0.291 0.503 0.178 0.030 -0.000 0.5285927386 346 0.353 -0.291 0.503 0.178 0.030 -0.000 0.5285927175 356 0.353 -0.291 0.503 0.178 0.030 -0.000 0.5285927109 358 0.353 -0.291 0.503 0.178 0.030 -0.000 0.5285925402 361 0.353 -0.291 0.503 0.178 0.030 -0.000 0.5285925108 429 0.353 -0.291 0.503 0.178 0.029 -0.000 0.5285919299 438 0.353 -0.291 0.502 0.178 0.029 -0.000 0.5285918357 493 0.353 -0.291 0.502 0.178 0.029 -0.000 0.5285917322 596 0.353 -0.291 0.503 0.178 0.029 -0.000 0.5285917236 597 0.353 -0.291 0.503 0.178 0.029 -0.000 0.5285917221 683 0.353 -0.291 0.503 0.178 0.029 -0.000 0.5285916892 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.019503 1 -25.0 -25.0 25.0 1.011064 2 -25.0 25.0 -25.0 1.018606 3 -25.0 25.0 25.0 0.998160 4 25.0 -25.0 -25.0 0.970753 5 25.0 -25.0 25.0 1.022585 6 25.0 25.0 -25.0 1.034141 7 25.0 25.0 25.0 0.942023 REL: 8 0.528592 8.016835 1.002104 rel = 0.527482 Number of iterations 7 Min cost was 0.528592 Number of FunctionCalls 728 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 24.169000 sec Parameters at optimum (transmm) 0.35306 -0.29075 0.50253 Parameters at optimum (rotdeg) 0.17813 0.02858 -0.00027 Final costs ---------------- Number of surface hits 27863 WM Intensity 1150.3812 +/- 287.2242 Ctx Intensity 1291.1200 +/- 300.3047 Pct Contrast 11.4094 +/- 35.8855 Cost 0.5286 RelCost 0.5675 Reg at min cost was 0.036 0.951 0.306 0.153; 0.999 -0.030 -0.023 39.710; -0.012 0.306 -0.952 -0.212; 0.000 0.000 0.000 1.000; Writing optimal reg to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat, type = 14 Original Reg 0.036 0.951 0.306 -0.200; 0.999 -0.029 -0.026 39.998; -0.016 0.307 -0.952 -0.839; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.000 0.000 -0.353; -0.000 0.001 -0.003 0.288; -0.003 0.001 0.000 -0.627; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.699257 Computing change in rh position Surface RMS Diff (mm) 0.773573 0.976707 mri_segreg done tkregister2_cmdl --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat --noedit --ltaout /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta tkregister_tcl /usr/local/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz reg file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.036 0.951 0.306 0.153; 0.999 -0.030 -0.023 39.710; -0.012 0.306 -0.952 -0.212; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz Tmov: -------------------- -0.977 0.000 0.000 125.000; 0.000 0.000 1.000 -6.499; 0.000 -0.977 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.036 0.951 0.306 0.153; 0.999 -0.030 -0.023 39.710; -0.012 0.306 -0.952 -0.212; 0.000 0.000 0.000 1.000; Determinant 1 subject = Andre_v_5_3 RegMat --------------------------- 0.036 0.951 0.306 0.153; 0.999 -0.030 -0.023 39.710; -0.012 0.306 -0.952 -0.212; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 0.001 0.002 1.225; -0.001 1.000 0.003 -0.187; -0.002 -0.003 1.000 -0.252; 0.000 0.000 0.000 1.000; transformed matrix: 0.035 -0.012 -0.999 171.256; 0.299 -0.930 0.023 207.956; -0.929 -0.299 -0.030 286.543; 0.000 0.000 0.000 1.000; Cleaning up Started at Tue Oct 14 13:33:49 CEST 2014 Ended at Tue Oct 14 13:34:53 CEST 2014 BBR-Run-Time-Sec 64 bbregister Done To check results, run: tkregister2 --mov /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz --reg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.dat --surf mri_convert -odt short -at /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta -rt cubic -ns 1 -rl /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.prenorm.mgz mri_convert -odt short -at /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta -rt cubic -ns 1 -rl /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.prenorm.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) INFO: Reading transformation from file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta... Reading transform with LTAreadEx() reading extra input line subject Andre_v_5_3 reading extra input line fscale 0.150000 reading template info from volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig.mgz... INFO: Applying transformation from file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/transforms/FLAIRraw.lta... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.000 0.001 0.002 1.225; -0.001 1.000 0.003 -0.187; -0.002 -0.003 1.000 -0.252; 0.000 0.000 0.000 1.000; --------------------------------- Applying LTAtransformInterp (resample_type 5) MRItoBSpline degree 3 changing data type from float to short (noscale = 1)... writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.prenorm.mgz... mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz -surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.white identity.nofile -surface /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.white identity.nofile /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.prenorm.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.mgz using Gaussian smoothing of bias field, sigma=0.500 disabling nonmaximum suppression retaining points that are at least 1.000mm from the boundary using segmentation for initial intensity normalization reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.prenorm.mgz... computing distance transform computing distance transform 92769 non wm control points removed building Voronoi diagram... performing soap bubble smoothing, sigma = 0... smoothing bias field writing normalized volume to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/FLAIR.mgz /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts cp -v /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.woFLAIR.pial `/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial' -> `/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 Andre_v_5_3 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.26 (0.06-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 3 with 5 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 deleting segment 6 with 797 points - only 0.00% unknown deleting segment 7 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown deleting segment 16 with 11 points - only 0.00% unknown deleting segment 17 with 13 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown deleting segment 19 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=psyk-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 32002 surface locations found to contain inconsistent values (30710 in, 1292 out) tol=1.0e-04, sigma=2.0, host=psyk-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=492825.1, rms=0.85 001: dt: 0.5000, sse=473009.9, rms=0.830 (0.000%) 002: dt: 0.5000, sse=457837.8, rms=0.810 (0.000%) 003: dt: 0.5000, sse=446869.2, rms=0.790 (0.000%) 004: dt: 0.5000, sse=438133.7, rms=0.771 (0.000%) 005: dt: 0.5000, sse=431619.3, rms=0.751 (0.000%) 006: dt: 0.5000, sse=426308.8, rms=0.732 (0.000%) 007: dt: 0.5000, sse=422217.6, rms=0.713 (0.000%) 008: dt: 0.5000, sse=418859.5, rms=0.694 (0.000%) 009: dt: 0.5000, sse=416280.7, rms=0.675 (0.000%) 010: dt: 0.5000, sse=414249.3, rms=0.657 (0.000%) 011: dt: 0.5000, sse=412948.7, rms=0.638 (0.000%) 012: dt: 0.5000, sse=411985.2, rms=0.620 (0.000%) 013: dt: 0.5000, sse=411229.3, rms=0.602 (0.000%) 014: dt: 0.5000, sse=411054.8, rms=0.585 (0.000%) 015: dt: 0.5000, sse=411089.5, rms=0.567 (0.000%) 016: dt: 0.5000, sse=411608.8, rms=0.550 (0.000%) 017: dt: 0.5000, sse=412100.0, rms=0.533 (0.000%) 018: dt: 0.5000, sse=412816.1, rms=0.516 (0.000%) 019: dt: 0.5000, sse=413704.2, rms=0.500 (0.000%) 020: dt: 0.5000, sse=414759.9, rms=0.484 (0.000%) 021: dt: 0.5000, sse=415866.2, rms=0.468 (0.000%) 022: dt: 0.5000, sse=416760.1, rms=0.452 (0.000%) 023: dt: 0.5000, sse=417656.8, rms=0.437 (0.000%) 024: dt: 0.5000, sse=418877.3, rms=0.423 (0.000%) 025: dt: 0.5000, sse=419421.2, rms=0.408 (0.000%) 026: dt: 0.5000, sse=419779.8, rms=0.394 (0.000%) 027: dt: 0.5000, sse=419937.9, rms=0.381 (0.000%) 028: dt: 0.5000, sse=420249.0, rms=0.368 (0.000%) 029: dt: 0.5000, sse=419621.4, rms=0.355 (0.000%) 030: dt: 0.5000, sse=419715.7, rms=0.343 (0.000%) positioning took 2.5 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 23733 surface locations found to contain inconsistent values (21720 in, 2013 out) tol=1.0e-04, sigma=1.0, host=psyk-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=76060.1, rms=0.53 031: dt: 0.5000, sse=74210.9, rms=0.519 (0.000%) 032: dt: 0.5000, sse=72951.3, rms=0.501 (0.000%) 033: dt: 0.5000, sse=71997.9, rms=0.484 (0.000%) 034: dt: 0.5000, sse=71292.3, rms=0.468 (0.000%) 035: dt: 0.5000, sse=70719.9, rms=0.453 (0.000%) 036: dt: 0.5000, sse=70263.6, rms=0.437 (0.000%) 037: dt: 0.5000, sse=70009.0, rms=0.422 (0.000%) 038: dt: 0.5000, sse=69921.4, rms=0.407 (0.000%) 039: dt: 0.5000, sse=69981.5, rms=0.392 (0.000%) 040: dt: 0.5000, sse=70310.4, rms=0.378 (0.000%) 041: dt: 0.5000, sse=70764.2, rms=0.364 (0.000%) 042: dt: 0.5000, sse=71342.4, rms=0.351 (0.000%) 043: dt: 0.5000, sse=71981.9, rms=0.337 (0.000%) 044: dt: 0.5000, sse=72718.6, rms=0.324 (0.000%) 045: dt: 0.5000, sse=73608.1, rms=0.312 (0.000%) 046: dt: 0.5000, sse=74406.1, rms=0.300 (0.000%) 047: dt: 0.5000, sse=75317.2, rms=0.289 (0.000%) 048: dt: 0.5000, sse=76197.1, rms=0.277 (0.000%) 049: dt: 0.5000, sse=77063.8, rms=0.266 (0.000%) 050: dt: 0.5000, sse=78011.5, rms=0.256 (0.000%) 051: dt: 0.5000, sse=79018.9, rms=0.247 (0.000%) 052: dt: 0.5000, sse=80066.4, rms=0.238 (0.000%) 053: dt: 0.5000, sse=80809.4, rms=0.229 (0.000%) 054: dt: 0.5000, sse=81567.4, rms=0.221 (0.000%) 055: dt: 0.5000, sse=82304.9, rms=0.213 (0.000%) 056: dt: 0.5000, sse=82934.8, rms=0.206 (0.000%) 057: dt: 0.5000, sse=83586.9, rms=0.199 (0.000%) 058: dt: 0.5000, sse=84114.2, rms=0.193 (0.000%) 059: dt: 0.5000, sse=84569.9, rms=0.186 (0.000%) 060: dt: 0.5000, sse=85082.7, rms=0.181 (0.000%) positioning took 2.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 15390 surface locations found to contain inconsistent values (12555 in, 2835 out) tol=1.0e-04, sigma=0.5, host=psyk-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=18885.6, rms=0.29 061: dt: 0.5000, sse=18476.0, rms=0.286 (0.000%) 062: dt: 0.5000, sse=17924.3, rms=0.277 (0.000%) 063: dt: 0.5000, sse=17509.7, rms=0.270 (0.000%) 064: dt: 0.5000, sse=17116.5, rms=0.263 (0.000%) 065: dt: 0.5000, sse=16756.3, rms=0.256 (0.000%) 066: dt: 0.5000, sse=16437.1, rms=0.250 (0.000%) 067: dt: 0.5000, sse=16125.6, rms=0.243 (0.000%) 068: dt: 0.5000, sse=15831.0, rms=0.237 (0.000%) 069: dt: 0.5000, sse=15574.7, rms=0.232 (0.000%) 070: dt: 0.5000, sse=15321.3, rms=0.226 (0.000%) 071: dt: 0.5000, sse=15107.1, rms=0.221 (0.000%) 072: dt: 0.5000, sse=14922.1, rms=0.216 (0.000%) 073: dt: 0.5000, sse=14773.0, rms=0.212 (0.000%) 074: dt: 0.5000, sse=14604.5, rms=0.208 (0.000%) 075: dt: 0.5000, sse=14416.1, rms=0.203 (0.000%) 076: dt: 0.5000, sse=14304.8, rms=0.199 (0.000%) 077: dt: 0.5000, sse=14181.9, rms=0.196 (0.000%) 078: dt: 0.5000, sse=14095.7, rms=0.193 (0.000%) 079: dt: 0.5000, sse=13986.8, rms=0.189 (0.000%) 080: dt: 0.5000, sse=13889.4, rms=0.186 (0.000%) 081: dt: 0.5000, sse=13816.7, rms=0.184 (0.000%) 082: dt: 0.5000, sse=13751.8, rms=0.182 (0.000%) 083: dt: 0.5000, sse=13699.3, rms=0.179 (0.000%) 084: dt: 0.5000, sse=13674.8, rms=0.177 (0.000%) 085: dt: 0.5000, sse=13606.9, rms=0.175 (0.000%) 086: dt: 0.5000, sse=13566.6, rms=0.174 (0.000%) 087: dt: 0.5000, sse=13526.9, rms=0.172 (0.000%) 088: dt: 0.5000, sse=13515.4, rms=0.171 (0.000%) 089: dt: 0.5000, sse=13451.0, rms=0.169 (0.000%) 090: dt: 0.5000, sse=13411.6, rms=0.168 (0.000%) positioning took 2.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 13238 surface locations found to contain inconsistent values (10148 in, 3090 out) tol=1.0e-04, sigma=0.2, host=psyk-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6391.2, rms=0.21 091: dt: 0.5000, sse=6307.5, rms=0.205 (0.000%) 092: dt: 0.5000, sse=6070.2, rms=0.200 (0.000%) 093: dt: 0.5000, sse=5960.2, rms=0.198 (0.000%) 094: dt: 0.5000, sse=5814.8, rms=0.195 (0.000%) 095: dt: 0.5000, sse=5694.8, rms=0.193 (0.000%) 096: dt: 0.5000, sse=5568.4, rms=0.190 (0.000%) 097: dt: 0.5000, sse=5458.8, rms=0.188 (0.000%) 098: dt: 0.5000, sse=5360.7, rms=0.186 (0.000%) 099: dt: 0.5000, sse=5268.0, rms=0.183 (0.000%) 100: dt: 0.5000, sse=5189.0, rms=0.182 (0.000%) 101: dt: 0.5000, sse=5082.8, rms=0.179 (0.000%) 102: dt: 0.5000, sse=5033.3, rms=0.178 (0.000%) 103: dt: 0.5000, sse=4991.2, rms=0.177 (0.000%) 104: dt: 0.5000, sse=4932.2, rms=0.176 (0.000%) 105: dt: 0.5000, sse=4870.8, rms=0.174 (0.000%) 106: dt: 0.5000, sse=4849.9, rms=0.174 (0.000%) 107: dt: 0.5000, sse=4805.0, rms=0.173 (0.000%) 108: dt: 0.5000, sse=4768.1, rms=0.172 (0.000%) 109: dt: 0.5000, sse=4710.1, rms=0.171 (0.000%) 110: dt: 0.5000, sse=4653.6, rms=0.169 (0.000%) 111: dt: 0.5000, sse=4651.7, rms=0.169 (0.000%) 112: dt: 0.5000, sse=4613.7, rms=0.168 (0.000%) 113: dt: 0.5000, sse=4595.6, rms=0.168 (0.000%) 114: dt: 0.5000, sse=4579.3, rms=0.167 (0.000%) 115: dt: 0.5000, sse=4556.7, rms=0.167 (0.000%) 116: dt: 0.5000, sse=4543.0, rms=0.167 (0.000%) 117: dt: 0.5000, sse=4515.4, rms=0.166 (0.000%) 118: dt: 0.5000, sse=4500.7, rms=0.165 (0.000%) 119: dt: 0.5000, sse=4502.4, rms=0.165 (0.000%) 120: dt: 0.5000, sse=4468.9, rms=0.165 (0.000%) positioning took 2.4 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area.pial vertex spacing 1.06 +- 0.45 (0.09-->7.00) (max @ vno 98589 --> 98572) face area 0.43 +- 0.31 (0.00-->8.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed thickness calculation complete, 348:713 truncations. 67484 vertices at 0 distance 98737 vertices at 1 distance 60722 vertices at 2 distance 18863 vertices at 3 distance 5140 vertices at 4 distance 1510 vertices at 5 distance 521 vertices at 6 distance 190 vertices at 7 distance 64 vertices at 8 distance 42 vertices at 9 distance 24 vertices at 10 distance 22 vertices at 11 distance 14 vertices at 12 distance 18 vertices at 13 distance 9 vertices at 14 distance 6 vertices at 15 distance 3 vertices at 16 distance 3 vertices at 17 distance 4 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.thickness positioning took 12.1 minutes /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts cp -v /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.woFLAIR.pial `/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial' -> `/net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.woFLAIR.pial' mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 Andre_v_5_3 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.26 (0.01-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown deleting segment 8 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 12 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=psyk-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. HISTOalloc(-2147483648): could not allocate histogram 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz compressed histogram detected, changing bin size to 0.000000 Cannot allocate memory Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Andre_v_5_3 exited with ERRORS at Tue Oct 14 13:49:18 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Oct 14 14:22:51 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 /usr/local/freesurfer/bin/recon-all -autorecon3 -s Andre_v_5_3 -FLAIR test_output_Andre/FLAIR/flair.nii -FLAIRpial -bbr-init-header subjid Andre_v_5_3 setenv SUBJECTS_DIR /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014 FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 49416388 24051656 25364732 16268 286704 21157380 -/+ buffers/cache: 2607572 46808816 Swap: 10485756 0 10485756 ######################################## program versions used $Id: recon-all,v 1.482 2014/08/26 20:36:16 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/10/14-12:22:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: evaghi Machine: psyk-stud140.uio.no Platform: Linux PlatformVersion: 2.6.32-431.29.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# T2/FLAIR Input Tue Oct 14 14:22:54 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3 mri_convert --no_scale 1 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz mri_convert --no_scale 1 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/test_output_Andre/FLAIR/flair.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0344518, -0.950483, -0.30886) j_ras = (0.0106435, -0.309375, 0.950881) k_ras = (0.99935, -0.0294721, -0.0207749) writing to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/orig/FLAIRraw.mgz... #----------------------------------------- #@# Curvature Stats lh Tue Oct 14 14:22:55 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 249 ] Gb_filter = 0 WARN: S lookup min: -0.327954 WARN: S explicit min: 0.000000 vertex = 144 #-------------------------------------------- #@# Sphere lh Tue Oct 14 14:22:58 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.53 pass 1: epoch 2 of 3 starting distance error %19.55 unfolding complete - removing small folds... starting distance error %19.46 removing remaining folds... final distance error %19.48 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.73 hours #-------------------------------------------- #@# Surf Reg lh Tue Oct 14 15:06:50 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.602 curvature mean = 0.041, std = 0.932 curvature mean = 0.008, std = 0.869 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 307117.9, tmin=0.8045 d=32.00 min @ (0.00, 8.00, 0.00) sse = 226073.8, tmin=1.6164 d=16.00 min @ (0.00, 0.00, 4.00) sse = 211214.2, tmin=2.4332 d=4.00 min @ (1.00, 0.00, -1.00) sse = 210319.8, tmin=4.0891 d=2.00 min @ (-0.50, -0.50, 0.00) sse = 209823.5, tmin=4.9296 d=1.00 min @ (0.00, 0.25, 0.25) sse = 209721.6, tmin=5.7685 d=0.50 min @ (0.00, 0.00, -0.12) sse = 209715.5, tmin=6.6242 tol=1.0e+00, sigma=0.5, host=psyk-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.62 min curvature mean = 0.022, std = 0.950 curvature mean = 0.004, std = 0.946 curvature mean = 0.019, std = 0.961 curvature mean = 0.002, std = 0.976 curvature mean = 0.018, std = 0.964 curvature mean = 0.000, std = 0.990 2 Reading smoothwm curvature mean = -0.019, std = 0.253 curvature mean = 0.005, std = 0.067 curvature mean = 0.043, std = 0.380 curvature mean = 0.005, std = 0.079 curvature mean = 0.027, std = 0.580 curvature mean = 0.005, std = 0.086 curvature mean = 0.015, std = 0.719 curvature mean = 0.005, std = 0.088 curvature mean = 0.005, std = 0.823 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 1113: 33 negative triangles #-------------------------------------------- #@# Jacobian white lh Tue Oct 14 15:35:51 CEST 2014 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Tue Oct 14 15:35:52 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Tue Oct 14 15:35:54 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 lh ../surf/lh.sphere.reg /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1458 labels changed using aseg relabeling using gibbs priors... 000: 2902 changed, 133935 examined... 001: 673 changed, 12460 examined... 002: 171 changed, 3779 examined... 003: 43 changed, 1038 examined... 004: 15 changed, 278 examined... 005: 6 changed, 101 examined... 006: 0 changed, 40 examined... 255 labels changed using aseg 000: 108 total segments, 67 labels (266 vertices) changed 001: 43 total segments, 4 labels (12 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 54 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 847 vertices marked for relabeling... 847 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 46 seconds. #-------------------------------------------- #@# Make Pial Surf lh Tue Oct 14 15:36:40 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.21 (0.06-->3.71) (max @ vno 100459 --> 106413) face area 0.29 +- 0.12 (0.00-->1.27) mean absolute distance = 0.79 +- 0.96 3792 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 130 points - only 14.62% unknown removing 2 vertex label from ripped group deleting segment 1 with 2 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 831 points - only 0.00% unknown deleting segment 5 with 45 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown deleting segment 7 with 40 points - only 0.00% unknown deleting segment 8 with 6 points - only 0.00% unknown deleting segment 9 with 11 points - only 0.00% unknown deleting segment 10 with 13 points - only 0.00% unknown deleting segment 11 with 49 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown mean border=69.0, 141 (141) missing vertices, mean dist 0.5 [0.7 (%22.6)->0.8 (%77.4))] %63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.94 +- 0.27 (0.10-->3.15) (max @ vno 69317 --> 69300) face area 0.29 +- 0.14 (0.00-->1.64) mean absolute distance = 0.34 +- 0.72 2450 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7931433.0, rms=15.08 001: dt: 0.5000, sse=6935160.0, rms=11.406 (0.000%) 002: dt: 0.5000, sse=6544342.5, rms=8.907 (0.000%) 003: dt: 0.5000, sse=6586972.0, rms=7.155 (0.000%) 004: dt: 0.5000, sse=6627329.5, rms=5.998 (0.000%) 005: dt: 0.5000, sse=6865879.0, rms=5.255 (0.000%) 006: dt: 0.5000, sse=6919816.5, rms=4.836 (0.000%) 007: dt: 0.5000, sse=7114851.5, rms=4.565 (0.000%) 008: dt: 0.5000, sse=7097618.5, rms=4.438 (0.000%) 009: dt: 0.5000, sse=7203923.0, rms=4.325 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7126259.0, rms=4.290 (0.000%) 011: dt: 0.2500, sse=4362082.0, rms=2.797 (0.000%) 012: dt: 0.2500, sse=3801983.2, rms=2.360 (0.000%) 013: dt: 0.2500, sse=3582298.0, rms=2.212 (0.000%) 014: dt: 0.2500, sse=3481731.8, rms=2.118 (0.000%) 015: dt: 0.2500, sse=3421952.2, rms=2.059 (0.000%) rms = 2.02, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=3381572.5, rms=2.015 (0.000%) 017: dt: 0.1250, sse=3263632.2, rms=1.881 (0.000%) rms = 1.86, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=3235483.2, rms=1.861 (0.000%) positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 161 points - only 17.39% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 4 with 645 points - only 0.00% unknown deleting segment 6 with 37 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 20 points - only 0.00% unknown deleting segment 9 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 11 with 4 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown deleting segment 13 with 17 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 16 with 61 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 4 points - only 0.00% unknown mean border=72.2, 79 (46) missing vertices, mean dist -0.2 [0.4 (%70.0)->0.3 (%30.0))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.12-->3.28) (max @ vno 93103 --> 92209) face area 0.37 +- 0.17 (0.00-->1.96) mean absolute distance = 0.29 +- 0.53 2944 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3970987.0, rms=5.17 019: dt: 0.5000, sse=4454506.0, rms=3.513 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=3973708.8, rms=2.475 (0.000%) 021: dt: 0.2500, sse=3767152.8, rms=1.990 (0.000%) 022: dt: 0.2500, sse=3656728.5, rms=1.727 (0.000%) rms = 1.69, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3623260.8, rms=1.686 (0.000%) 024: dt: 0.1250, sse=3536692.2, rms=1.560 (0.000%) rms = 1.54, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3505861.5, rms=1.540 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 168 points - only 16.67% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown deleting segment 3 with 686 points - only 0.00% unknown deleting segment 4 with 40 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 30 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown deleting segment 12 with 57 points - only 0.00% unknown deleting segment 13 with 8 points - only 0.00% unknown mean border=75.1, 77 (43) missing vertices, mean dist -0.2 [0.3 (%68.3)->0.2 (%31.7))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.13-->3.56) (max @ vno 111457 --> 111456) face area 0.36 +- 0.16 (0.00-->2.01) mean absolute distance = 0.25 +- 0.41 2338 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3865593.2, rms=4.13 026: dt: 0.5000, sse=4328042.5, rms=3.538 (0.000%) rms = 3.87, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3907882.5, rms=2.334 (0.000%) 028: dt: 0.2500, sse=3723624.5, rms=1.850 (0.000%) 029: dt: 0.2500, sse=3709880.0, rms=1.549 (0.000%) rms = 1.55, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3699352.5, rms=1.545 (0.000%) 031: dt: 0.1250, sse=3626586.0, rms=1.384 (0.000%) rms = 1.36, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3604916.5, rms=1.365 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 175 points - only 16.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 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 712 points - only 0.00% unknown deleting segment 5 with 44 points - only 0.00% unknown deleting segment 6 with 40 points - only 0.00% unknown deleting segment 7 with 36 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 9 with 10 points - only 0.00% unknown deleting segment 10 with 18 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 11 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 60 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown mean border=76.3, 81 (39) missing vertices, mean dist -0.1 [0.3 (%56.8)->0.2 (%43.2))] %81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3669868.8, rms=2.21 rms = 2.63, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3762752.2, rms=1.531 (0.000%) 034: dt: 0.2500, sse=3948763.2, rms=1.104 (0.000%) rms = 1.06, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=3999052.2, rms=1.059 (0.000%) rms = 1.04, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=4031869.2, rms=1.039 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 16 points - only 25.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 5 points - only 20.00% unknown smoothing surface for 5 iterations... mean border=44.7, 108 (108) missing vertices, mean dist 1.7 [0.0 (%0.0)->2.0 (%100.0))] %14 local maxima, %66 large gradients and %15 min vals, 1713 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27774222.0, rms=31.55 001: dt: 0.5000, sse=19744250.0, rms=26.075 (0.000%) 002: dt: 0.5000, sse=14127545.0, rms=21.462 (0.000%) 003: dt: 0.5000, sse=10548771.0, rms=17.785 (0.000%) 004: dt: 0.5000, sse=8627045.0, rms=14.803 (0.000%) 005: dt: 0.5000, sse=7348371.5, rms=12.299 (0.000%) 006: dt: 0.5000, sse=6612727.0, rms=10.273 (0.000%) 007: dt: 0.5000, sse=6053383.0, rms=8.576 (0.000%) 008: dt: 0.5000, sse=5788639.0, rms=7.187 (0.000%) 009: dt: 0.5000, sse=5610497.5, rms=6.077 (0.000%) 010: dt: 0.5000, sse=5643526.5, rms=5.275 (0.000%) 011: dt: 0.5000, sse=5587664.0, rms=4.732 (0.000%) 012: dt: 0.5000, sse=5703336.0, rms=4.397 (0.000%) 013: dt: 0.5000, sse=5683819.0, rms=4.153 (0.000%) 014: dt: 0.5000, sse=5771044.0, rms=3.999 (0.000%) 015: dt: 0.5000, sse=5726464.5, rms=3.881 (0.000%) 016: dt: 0.5000, sse=5811575.0, rms=3.800 (0.000%) 017: dt: 0.5000, sse=5761283.5, rms=3.730 (0.000%) 018: dt: 0.5000, sse=5797567.0, rms=3.675 (0.000%) rms = 3.64, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=5756588.5, rms=3.635 (0.000%) 020: dt: 0.2500, sse=3891133.2, rms=2.857 (0.000%) 021: dt: 0.2500, sse=3675003.8, rms=2.687 (0.000%) rms = 2.64, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3579567.8, rms=2.641 (0.000%) 023: dt: 0.1250, sse=3450344.5, rms=2.556 (0.000%) rms = 2.55, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3435661.8, rms=2.546 (0.000%) positioning took 2.0 minutes mean border=42.7, 472 (28) missing vertices, mean dist 0.2 [0.2 (%54.3)->0.8 (%45.7))] %33 local maxima, %51 large gradients and %11 min vals, 605 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4060163.5, rms=4.82 025: dt: 0.5000, sse=4331332.5, rms=3.821 (0.000%) 026: dt: 0.5000, sse=5401962.0, rms=3.678 (0.000%) 027: dt: 0.5000, sse=5601610.0, rms=3.578 (0.000%) rms = 3.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4500867.0, rms=2.911 (0.000%) 029: dt: 0.2500, sse=4218836.0, rms=2.637 (0.000%) 030: dt: 0.2500, sse=4089517.2, rms=2.547 (0.000%) rms = 2.51, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=4061397.5, rms=2.515 (0.000%) 032: dt: 0.1250, sse=3957642.5, rms=2.438 (0.000%) rms = 2.43, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3947623.5, rms=2.426 (0.000%) positioning took 0.8 minutes mean border=40.4, 678 (23) missing vertices, mean dist 0.2 [0.2 (%43.4)->0.5 (%56.6))] %51 local maxima, %33 large gradients and %10 min vals, 678 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4268281.0, rms=4.13 034: dt: 0.5000, sse=4423501.5, rms=3.341 (0.000%) rms = 3.36, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=4168684.0, rms=2.780 (0.000%) 036: dt: 0.2500, sse=4205171.5, rms=2.458 (0.000%) 037: dt: 0.2500, sse=4173098.5, rms=2.378 (0.000%) rms = 2.34, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4184372.2, rms=2.341 (0.000%) 039: dt: 0.1250, sse=4097827.0, rms=2.291 (0.000%) rms = 2.28, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=4094593.8, rms=2.283 (0.000%) positioning took 0.6 minutes mean border=38.8, 1433 (17) missing vertices, mean dist 0.1 [0.2 (%44.7)->0.4 (%55.3))] %61 local maxima, %22 large gradients and %10 min vals, 636 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4201795.5, rms=3.02 rms = 3.05, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=4079617.0, rms=2.582 (0.000%) 042: dt: 0.2500, sse=4110240.2, rms=2.267 (0.000%) 043: dt: 0.2500, sse=4164422.8, rms=2.161 (0.000%) rms = 2.12, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=4187721.8, rms=2.118 (0.000%) rms = 2.07, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4126205.8, rms=2.073 (0.000%) positioning took 0.5 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area.pial vertex spacing 1.03 +- 0.42 (0.08-->7.11) (max @ vno 99529 --> 98590) face area 0.43 +- 0.31 (0.00-->8.42) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed thickness calculation complete, 568:1039 truncations. 39591 vertices at 0 distance 100082 vertices at 1 distance 77896 vertices at 2 distance 25453 vertices at 3 distance 6940 vertices at 4 distance 2124 vertices at 5 distance 713 vertices at 6 distance 268 vertices at 7 distance 106 vertices at 8 distance 52 vertices at 9 distance 45 vertices at 10 distance 28 vertices at 11 distance 18 vertices at 12 distance 16 vertices at 13 distance 7 vertices at 14 distance 12 vertices at 15 distance 6 vertices at 16 distance 2 vertices at 17 distance 7 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.thickness positioning took 10.1 minutes #-------------------------------------------- #@# Surf Volume lh Tue Oct 14 15:46:44 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# Curvature Stats rh Tue Oct 14 15:46:44 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Andre_v_5_3 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 [ Andre_v_5_3/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 [ 255 ] Gb_filter = 0 WARN: S lookup min: -0.384488 WARN: S explicit min: 0.000000 vertex = 1125 #-------------------------------------------- #@# Sphere rh Tue Oct 14 15:46:48 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.301... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=psyk-, 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 %19.82 pass 1: epoch 2 of 3 starting distance error %19.77 unfolding complete - removing small folds... starting distance error %19.67 removing remaining folds... final distance error %19.69 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.69 hours #-------------------------------------------- #@# Surf Reg rh Tue Oct 14 16:28:16 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=psyk-, 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=psyk-, 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 = 0.612 curvature mean = 0.032, std = 0.933 curvature mean = 0.009, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, -16.00) sse = 392863.9, tmin=0.8095 d=32.00 min @ (8.00, 8.00, 8.00) sse = 299372.4, tmin=1.6268 d=16.00 min @ (-4.00, 0.00, -4.00) sse = 281465.4, tmin=2.4583 d=8.00 min @ (2.00, 2.00, 2.00) sse = 272550.2, tmin=3.3130 d=2.00 min @ (0.00, -0.50, -0.50) sse = 271783.1, tmin=5.0477 d=1.00 min @ (0.25, 0.00, 0.00) sse = 271765.7, tmin=5.9072 d=0.50 min @ (0.00, 0.12, 0.12) sse = 271743.5, tmin=6.7693 tol=1.0e+00, sigma=0.5, host=psyk-, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 6.77 min curvature mean = 0.004, std = 0.935 curvature mean = 0.003, std = 0.945 curvature mean = -0.002, std = 0.944 curvature mean = 0.002, std = 0.975 curvature mean = -0.003, std = 0.945 curvature mean = 0.000, std = 0.988 2 Reading smoothwm curvature mean = -0.020, std = 0.291 curvature mean = 0.007, std = 0.069 curvature mean = 0.037, std = 0.332 curvature mean = 0.007, std = 0.083 curvature mean = 0.024, std = 0.500 curvature mean = 0.007, std = 0.089 curvature mean = 0.014, std = 0.622 curvature mean = 0.007, std = 0.092 curvature mean = 0.004, std = 0.723 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Tue Oct 14 16:49:06 CEST 2014 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Tue Oct 14 16:49:08 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mrisp_paint -a 5 /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Tue Oct 14 16:49:09 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Andre_v_5_3 rh ../surf/rh.sphere.reg /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1442 labels changed using aseg relabeling using gibbs priors... 000: 2951 changed, 134598 examined... 001: 644 changed, 12684 examined... 002: 162 changed, 3674 examined... 003: 52 changed, 950 examined... 004: 20 changed, 328 examined... 005: 5 changed, 116 examined... 006: 4 changed, 38 examined... 007: 3 changed, 25 examined... 008: 2 changed, 19 examined... 009: 3 changed, 12 examined... 010: 0 changed, 11 examined... 167 labels changed using aseg 000: 110 total segments, 71 labels (288 vertices) changed 001: 40 total segments, 1 labels (7 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 47 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1282 vertices marked for relabeling... 1282 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 47 seconds. #-------------------------------------------- #@# Make Pial Surf rh Tue Oct 14 16:49:56 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Andre_v_5_3 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.83 +- 0.22 (0.01-->5.20) (max @ vno 72167 --> 134425) face area 0.29 +- 0.12 (0.00-->4.07) mean absolute distance = 0.81 +- 0.98 3159 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 212 points - only 18.40% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown deleting segment 7 with 372 points - only 9.41% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown deleting segment 10 with 80 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 12 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown mean border=68.9, 225 (223) missing vertices, mean dist 0.5 [0.7 (%22.9)->0.8 (%77.1))] %58 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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 0.95 +- 0.27 (0.13-->8.09) (max @ vno 72167 --> 134425) face area 0.29 +- 0.14 (0.00-->4.46) mean absolute distance = 0.36 +- 0.77 2612 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=8313815.0, rms=15.55 001: dt: 0.5000, sse=7146796.0, rms=11.809 (0.000%) 002: dt: 0.5000, sse=6781295.0, rms=9.310 (0.000%) 003: dt: 0.5000, sse=6751818.0, rms=7.551 (0.000%) 004: dt: 0.5000, sse=6797656.0, rms=6.386 (0.000%) 005: dt: 0.5000, sse=6938629.0, rms=5.638 (0.000%) 006: dt: 0.5000, sse=7114581.0, rms=5.212 (0.000%) 007: dt: 0.5000, sse=7213681.5, rms=4.944 (0.000%) 008: dt: 0.5000, sse=7301671.0, rms=4.821 (0.000%) 009: dt: 0.5000, sse=7308899.0, rms=4.706 (0.000%) rms = 4.66, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=7345646.0, rms=4.662 (0.000%) 011: dt: 0.2500, sse=4507853.0, rms=3.296 (0.000%) 012: dt: 0.2500, sse=3927899.2, rms=2.913 (0.000%) 013: dt: 0.2500, sse=3700164.5, rms=2.782 (0.000%) 014: dt: 0.2500, sse=3602761.5, rms=2.690 (0.000%) 015: dt: 0.2500, sse=3544500.2, rms=2.627 (0.000%) 016: dt: 0.2500, sse=3497563.5, rms=2.577 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=3469812.2, rms=2.535 (0.000%) 018: dt: 0.1250, sse=3345961.2, rms=2.397 (0.000%) rms = 2.37, time step reduction 3 of 3 to 0.062... 019: dt: 0.1250, sse=3315012.5, rms=2.370 (0.000%) positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 316 points - only 27.53% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 2 with 4 points - only 0.00% unknown deleting segment 5 with 22 points - only 0.00% unknown deleting segment 6 with 342 points - only 10.23% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown mean border=72.1, 208 (76) missing vertices, mean dist -0.2 [0.4 (%68.6)->0.2 (%31.4))] %65 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.94 +- 0.26 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.37 +- 0.17 (0.00-->5.95) mean absolute distance = 0.30 +- 0.56 2604 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063785.0, rms=5.40 020: dt: 0.5000, sse=4523467.0, rms=3.735 (0.000%) rms = 4.19, time step reduction 1 of 3 to 0.250... 021: dt: 0.2500, sse=4032946.2, rms=2.720 (0.000%) 022: dt: 0.2500, sse=3805957.8, rms=2.206 (0.000%) 023: dt: 0.2500, sse=3707945.8, rms=1.936 (0.000%) 024: dt: 0.2500, sse=3668042.2, rms=1.867 (0.000%) 025: dt: 0.2500, sse=3630981.5, rms=1.789 (0.000%) rms = 1.76, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3622747.5, rms=1.758 (0.000%) 027: dt: 0.1250, sse=3544567.0, rms=1.642 (0.000%) rms = 1.63, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3519431.2, rms=1.626 (0.000%) positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 273 points - only 21.98% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 3 with 3 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 25 points - only 0.00% unknown deleting segment 6 with 355 points - only 9.86% unknown removing 2 vertex label from ripped group deleting segment 7 with 2 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 9 with 3 points - only 0.00% unknown deleting segment 10 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 9 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=75.0, 213 (40) missing vertices, mean dist -0.2 [0.3 (%67.2)->0.2 (%32.8))] %74 local maxima, %20 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.93 +- 0.25 (0.09-->8.26) (max @ vno 72167 --> 134425) face area 0.36 +- 0.17 (0.00-->5.94) mean absolute distance = 0.25 +- 0.43 2596 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3888091.5, rms=4.21 029: dt: 0.5000, sse=4422753.5, rms=3.553 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3978346.2, rms=2.353 (0.000%) 031: dt: 0.2500, sse=3775159.0, rms=1.874 (0.000%) 032: dt: 0.2500, sse=3753626.8, rms=1.587 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 033: dt: 0.2500, sse=3742703.0, rms=1.581 (0.000%) 034: dt: 0.1250, sse=3663753.8, rms=1.402 (0.000%) rms = 1.38, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=3635901.0, rms=1.375 (0.000%) positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 260 points - only 22.31% unknown deleting segment 1 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 2 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 7 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown deleting segment 6 with 360 points - only 9.72% unknown removing 4 vertex label from ripped group deleting segment 7 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 10 with 3 points - only 0.00% unknown deleting segment 11 with 15 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 12 with 3 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 16 with 3 points - only 0.00% unknown mean border=76.2, 214 (38) missing vertices, mean dist -0.1 [0.3 (%55.9)->0.2 (%44.1))] %78 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3697700.8, rms=2.20 rms = 2.68, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=3792608.8, rms=1.495 (0.000%) 037: dt: 0.2500, sse=3992508.8, rms=1.111 (0.000%) rms = 1.08, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=4045497.2, rms=1.083 (0.000%) rms = 1.06, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4078604.5, rms=1.058 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 5 points - only 40.00% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 1 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=44.6, 185 (185) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.0 (%100.0))] %14 local maxima, %68 large gradients and %12 min vals, 1135 gradients ignored tol=1.0e-04, sigma=2.0, host=psyk-, 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=27757564.0, rms=31.51 001: dt: 0.5000, sse=19622334.0, rms=25.962 (0.000%) 002: dt: 0.5000, sse=13969531.0, rms=21.285 (0.000%) 003: dt: 0.5000, sse=10452963.0, rms=17.595 (0.000%) 004: dt: 0.5000, sse=8683913.0, rms=14.616 (0.000%) 005: dt: 0.5000, sse=7454407.0, rms=12.132 (0.000%) 006: dt: 0.5000, sse=6748061.5, rms=10.122 (0.000%) 007: dt: 0.5000, sse=6216010.0, rms=8.495 (0.000%) 008: dt: 0.5000, sse=6009703.5, rms=7.175 (0.000%) 009: dt: 0.5000, sse=5901022.5, rms=6.182 (0.000%) 010: dt: 0.5000, sse=5902673.5, rms=5.458 (0.000%) 011: dt: 0.5000, sse=5943038.5, rms=5.003 (0.000%) 012: dt: 0.5000, sse=6007918.0, rms=4.693 (0.000%) 013: dt: 0.5000, sse=6031596.5, rms=4.489 (0.000%) 014: dt: 0.5000, sse=6078880.0, rms=4.313 (0.000%) 015: dt: 0.5000, sse=6087874.5, rms=4.205 (0.000%) 016: dt: 0.5000, sse=6121907.5, rms=4.086 (0.000%) 017: dt: 0.5000, sse=6107810.0, rms=4.026 (0.000%) 018: dt: 0.5000, sse=6112403.5, rms=3.951 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=6106326.0, rms=3.924 (0.000%) 020: dt: 0.2500, sse=4101950.2, rms=3.083 (0.000%) 021: dt: 0.2500, sse=3851306.8, rms=2.892 (0.000%) 022: dt: 0.2500, sse=3748330.0, rms=2.840 (0.000%) rms = 2.82, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=3727270.0, rms=2.817 (0.000%) 024: dt: 0.1250, sse=3592225.0, rms=2.731 (0.000%) rms = 2.72, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3571643.8, rms=2.722 (0.000%) positioning took 2.1 minutes mean border=42.3, 540 (30) missing vertices, mean dist 0.3 [0.2 (%52.3)->0.8 (%47.7))] %35 local maxima, %50 large gradients and % 9 min vals, 343 gradients ignored tol=1.0e-04, sigma=1.0, host=psyk-, 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=4304544.5, rms=5.31 026: dt: 0.5000, sse=4590206.5, rms=4.247 (0.000%) 027: dt: 0.5000, sse=5616884.0, rms=4.038 (0.000%) 028: dt: 0.5000, sse=5905539.0, rms=3.948 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4744676.5, rms=3.233 (0.000%) 030: dt: 0.2500, sse=4440080.5, rms=2.929 (0.000%) 031: dt: 0.2500, sse=4299986.0, rms=2.827 (0.000%) rms = 2.78, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=4288588.5, rms=2.785 (0.000%) 033: dt: 0.1250, sse=4163390.2, rms=2.700 (0.000%) rms = 2.69, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=4147538.2, rms=2.686 (0.000%) positioning took 0.8 minutes mean border=39.8, 695 (21) missing vertices, mean dist 0.2 [0.2 (%42.0)->0.6 (%58.0))] %52 local maxima, %33 large gradients and % 8 min vals, 423 gradients ignored tol=1.0e-04, sigma=0.5, host=psyk-, 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=4533188.5, rms=4.56 035: dt: 0.5000, sse=4724519.5, rms=3.730 (0.000%) rms = 3.71, time step reduction 1 of 3 to 0.250... 036: dt: 0.5000, sse=5770925.0, rms=3.710 (0.000%) 037: dt: 0.2500, sse=4644892.5, rms=2.853 (0.000%) 038: dt: 0.2500, sse=4592182.5, rms=2.656 (0.000%) rms = 2.62, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4505625.5, rms=2.621 (0.000%) 040: dt: 0.1250, sse=4391475.5, rms=2.515 (0.000%) rms = 2.50, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4382284.5, rms=2.500 (0.000%) positioning took 0.6 minutes mean border=38.2, 1473 (10) missing vertices, mean dist 0.1 [0.2 (%44.1)->0.4 (%55.9))] %63 local maxima, %23 large gradients and % 8 min vals, 454 gradients ignored tol=1.0e-04, sigma=0.2, host=psyk-, 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 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4500635.0, rms=3.25 rms = 3.37, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=4368730.5, rms=2.816 (0.000%) 043: dt: 0.2500, sse=4366523.5, rms=2.539 (0.000%) 044: dt: 0.2500, sse=4431401.0, rms=2.440 (0.000%) rms = 2.40, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=4462294.5, rms=2.395 (0.000%) 046: dt: 0.1250, sse=4389830.0, rms=2.342 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=4388312.0, rms=2.324 (0.000%) positioning took 0.6 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.area.pial vertex spacing 1.04 +- 0.43 (0.03-->8.77) (max @ vno 101298 --> 101320) face area 0.43 +- 0.32 (0.00-->9.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed 0 of 134598 vertices processed 25000 of 134598 vertices processed 50000 of 134598 vertices processed 75000 of 134598 vertices processed 100000 of 134598 vertices processed 125000 of 134598 vertices processed thickness calculation complete, 593:1166 truncations. 43529 vertices at 0 distance 101643 vertices at 1 distance 75487 vertices at 2 distance 24049 vertices at 3 distance 6180 vertices at 4 distance 1804 vertices at 5 distance 613 vertices at 6 distance 225 vertices at 7 distance 93 vertices at 8 distance 44 vertices at 9 distance 37 vertices at 10 distance 18 vertices at 11 distance 23 vertices at 12 distance 15 vertices at 13 distance 20 vertices at 14 distance 12 vertices at 15 distance 5 vertices at 16 distance 0 vertices at 17 distance 3 vertices at 18 distance 1 vertices at 19 distance 1 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.thickness positioning took 10.5 minutes #-------------------------------------------- #@# Surf Volume rh Tue Oct 14 17:00:25 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/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_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #-------------------------------------------- #@# Refine Pial Surfs w/ T2/FLAIR Tue Oct 14 17:00:26 CEST 2014 /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 Andre_v_5_3 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 13504 bright wm thresholded. 276 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (91.0): 92.4 +- 9.4 [70.0 --> 110.0] GM (76.0) : 73.0 +- 14.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.9 (was 70) setting MAX_BORDER_WHITE to 110.4 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.8 (was 40) setting MAX_GRAY to 91.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.6 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=101, GM=55 mean inside = 90.5, mean outside = 68.0 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.26 (0.06-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 3 with 5 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 deleting segment 6 with 797 points - only 0.00% unknown deleting segment 7 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 37 points - only 0.00% unknown deleting segment 11 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown deleting segment 13 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 14 with 4 points - only 0.00% unknown deleting segment 15 with 6 points - only 0.00% unknown deleting segment 16 with 11 points - only 0.00% unknown deleting segment 17 with 13 points - only 0.00% unknown deleting segment 18 with 55 points - only 0.00% unknown deleting segment 19 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=psyk-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.92 +- 0.26 (0.09-->4.34) (max @ vno 98376 --> 99295) face area 0.35 +- 0.16 (0.00-->2.51) averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 148 points - only 20.27% unknown removing 3 vertex label from ripped group deleting segment 1 with 3 points - only 0.00% unknown deleting segment 2 with 5 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 3 with 2 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 4 with 4 points - only 0.00% unknown deleting segment 5 with 797 points - only 0.00% unknown deleting segment 6 with 45 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 8 with 37 points - only 0.00% unknown deleting segment 9 with 40 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 1 points - only 0.00% unknown deleting segment 11 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown deleting segment 15 with 13 points - only 0.00% unknown deleting segment 16 with 55 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3987848.8, rms=0.00 rms = 1.25, time step reduction 1 of 3 to 0.250... rms = 0.32, time step reduction 2 of 3 to 0.125... rms = 0.04, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=3987848.8, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 32002 surface locations found to contain inconsistent values (30710 in, 1292 out) tol=1.0e-04, sigma=2.0, host=psyk-, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.100, l_nspring=0.050, l_location=1.000, l_curv=0.100 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=492825.1, rms=0.85 001: dt: 0.5000, sse=473009.9, rms=0.830 (0.000%) 002: dt: 0.5000, sse=457837.8, rms=0.810 (0.000%) 003: dt: 0.5000, sse=446869.2, rms=0.790 (0.000%) 004: dt: 0.5000, sse=438133.7, rms=0.771 (0.000%) 005: dt: 0.5000, sse=431619.3, rms=0.751 (0.000%) 006: dt: 0.5000, sse=426308.8, rms=0.732 (0.000%) 007: dt: 0.5000, sse=422217.6, rms=0.713 (0.000%) 008: dt: 0.5000, sse=418859.5, rms=0.694 (0.000%) 009: dt: 0.5000, sse=416280.7, rms=0.675 (0.000%) 010: dt: 0.5000, sse=414249.3, rms=0.657 (0.000%) 011: dt: 0.5000, sse=412948.7, rms=0.638 (0.000%) 012: dt: 0.5000, sse=411985.2, rms=0.620 (0.000%) 013: dt: 0.5000, sse=411229.3, rms=0.602 (0.000%) 014: dt: 0.5000, sse=411054.8, rms=0.585 (0.000%) 015: dt: 0.5000, sse=411089.5, rms=0.567 (0.000%) 016: dt: 0.5000, sse=411608.8, rms=0.550 (0.000%) 017: dt: 0.5000, sse=412100.0, rms=0.533 (0.000%) 018: dt: 0.5000, sse=412816.1, rms=0.516 (0.000%) 019: dt: 0.5000, sse=413704.2, rms=0.500 (0.000%) 020: dt: 0.5000, sse=414759.9, rms=0.484 (0.000%) 021: dt: 0.5000, sse=415866.2, rms=0.468 (0.000%) 022: dt: 0.5000, sse=416760.1, rms=0.452 (0.000%) 023: dt: 0.5000, sse=417656.8, rms=0.437 (0.000%) 024: dt: 0.5000, sse=418877.3, rms=0.423 (0.000%) 025: dt: 0.5000, sse=419421.2, rms=0.408 (0.000%) 026: dt: 0.5000, sse=419779.8, rms=0.394 (0.000%) 027: dt: 0.5000, sse=419937.9, rms=0.381 (0.000%) 028: dt: 0.5000, sse=420249.0, rms=0.368 (0.000%) 029: dt: 0.5000, sse=419621.4, rms=0.355 (0.000%) 030: dt: 0.5000, sse=419715.7, rms=0.343 (0.000%) positioning took 2.5 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 23733 surface locations found to contain inconsistent values (21720 in, 2013 out) tol=1.0e-04, sigma=1.0, host=psyk-, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.010, l_nspring=0.005, l_location=1.000, l_curv=0.010 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=76060.1, rms=0.53 031: dt: 0.5000, sse=74210.9, rms=0.519 (0.000%) 032: dt: 0.5000, sse=72951.3, rms=0.501 (0.000%) 033: dt: 0.5000, sse=71997.9, rms=0.484 (0.000%) 034: dt: 0.5000, sse=71292.3, rms=0.468 (0.000%) 035: dt: 0.5000, sse=70719.9, rms=0.453 (0.000%) 036: dt: 0.5000, sse=70263.6, rms=0.437 (0.000%) 037: dt: 0.5000, sse=70009.0, rms=0.422 (0.000%) 038: dt: 0.5000, sse=69921.4, rms=0.407 (0.000%) 039: dt: 0.5000, sse=69981.5, rms=0.392 (0.000%) 040: dt: 0.5000, sse=70310.4, rms=0.378 (0.000%) 041: dt: 0.5000, sse=70764.2, rms=0.364 (0.000%) 042: dt: 0.5000, sse=71342.4, rms=0.351 (0.000%) 043: dt: 0.5000, sse=71981.9, rms=0.337 (0.000%) 044: dt: 0.5000, sse=72718.6, rms=0.324 (0.000%) 045: dt: 0.5000, sse=73608.1, rms=0.312 (0.000%) 046: dt: 0.5000, sse=74406.1, rms=0.300 (0.000%) 047: dt: 0.5000, sse=75317.2, rms=0.289 (0.000%) 048: dt: 0.5000, sse=76197.1, rms=0.277 (0.000%) 049: dt: 0.5000, sse=77063.8, rms=0.266 (0.000%) 050: dt: 0.5000, sse=78011.5, rms=0.256 (0.000%) 051: dt: 0.5000, sse=79018.9, rms=0.247 (0.000%) 052: dt: 0.5000, sse=80066.4, rms=0.238 (0.000%) 053: dt: 0.5000, sse=80809.4, rms=0.229 (0.000%) 054: dt: 0.5000, sse=81567.4, rms=0.221 (0.000%) 055: dt: 0.5000, sse=82304.9, rms=0.213 (0.000%) 056: dt: 0.5000, sse=82934.8, rms=0.206 (0.000%) 057: dt: 0.5000, sse=83586.9, rms=0.199 (0.000%) 058: dt: 0.5000, sse=84114.2, rms=0.193 (0.000%) 059: dt: 0.5000, sse=84569.9, rms=0.186 (0.000%) 060: dt: 0.5000, sse=85082.7, rms=0.181 (0.000%) positioning took 2.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 15390 surface locations found to contain inconsistent values (12555 in, 2835 out) tol=1.0e-04, sigma=0.5, host=psyk-, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.001, l_nspring=0.000, l_location=1.000, l_curv=0.001 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=18885.6, rms=0.29 061: dt: 0.5000, sse=18476.0, rms=0.286 (0.000%) 062: dt: 0.5000, sse=17924.3, rms=0.277 (0.000%) 063: dt: 0.5000, sse=17509.7, rms=0.270 (0.000%) 064: dt: 0.5000, sse=17116.5, rms=0.263 (0.000%) 065: dt: 0.5000, sse=16756.3, rms=0.256 (0.000%) 066: dt: 0.5000, sse=16437.1, rms=0.250 (0.000%) 067: dt: 0.5000, sse=16125.6, rms=0.243 (0.000%) 068: dt: 0.5000, sse=15831.0, rms=0.237 (0.000%) 069: dt: 0.5000, sse=15574.7, rms=0.232 (0.000%) 070: dt: 0.5000, sse=15321.3, rms=0.226 (0.000%) 071: dt: 0.5000, sse=15107.1, rms=0.221 (0.000%) 072: dt: 0.5000, sse=14922.1, rms=0.216 (0.000%) 073: dt: 0.5000, sse=14773.0, rms=0.212 (0.000%) 074: dt: 0.5000, sse=14604.5, rms=0.208 (0.000%) 075: dt: 0.5000, sse=14416.1, rms=0.203 (0.000%) 076: dt: 0.5000, sse=14304.8, rms=0.199 (0.000%) 077: dt: 0.5000, sse=14181.9, rms=0.196 (0.000%) 078: dt: 0.5000, sse=14095.7, rms=0.193 (0.000%) 079: dt: 0.5000, sse=13986.8, rms=0.189 (0.000%) 080: dt: 0.5000, sse=13889.4, rms=0.186 (0.000%) 081: dt: 0.5000, sse=13816.7, rms=0.184 (0.000%) 082: dt: 0.5000, sse=13751.8, rms=0.182 (0.000%) 083: dt: 0.5000, sse=13699.3, rms=0.179 (0.000%) 084: dt: 0.5000, sse=13674.8, rms=0.177 (0.000%) 085: dt: 0.5000, sse=13606.9, rms=0.175 (0.000%) 086: dt: 0.5000, sse=13566.6, rms=0.174 (0.000%) 087: dt: 0.5000, sse=13526.9, rms=0.172 (0.000%) 088: dt: 0.5000, sse=13515.4, rms=0.171 (0.000%) 089: dt: 0.5000, sse=13451.0, rms=0.169 (0.000%) 090: dt: 0.5000, sse=13411.6, rms=0.168 (0.000%) positioning took 2.4 minutes repositioning pial surface locations using ../mri/FLAIR.mgz locating cortical regions not in the range [-0.60 0.60], gm=0.00+-0.20, and vertices in regions > -0.1 13238 surface locations found to contain inconsistent values (10148 in, 3090 out) tol=1.0e-04, sigma=0.2, host=psyk-, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.000, l_nspring=0.000, l_location=1.000, l_curv=0.000 mom=0.00, dt=0.50 writing pial surface to /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6391.2, rms=0.21 091: dt: 0.5000, sse=6307.5, rms=0.205 (0.000%) 092: dt: 0.5000, sse=6070.2, rms=0.200 (0.000%) 093: dt: 0.5000, sse=5960.2, rms=0.198 (0.000%) 094: dt: 0.5000, sse=5814.8, rms=0.195 (0.000%) 095: dt: 0.5000, sse=5694.8, rms=0.193 (0.000%) 096: dt: 0.5000, sse=5568.4, rms=0.190 (0.000%) 097: dt: 0.5000, sse=5458.8, rms=0.188 (0.000%) 098: dt: 0.5000, sse=5360.7, rms=0.186 (0.000%) 099: dt: 0.5000, sse=5268.0, rms=0.183 (0.000%) 100: dt: 0.5000, sse=5189.0, rms=0.182 (0.000%) 101: dt: 0.5000, sse=5082.8, rms=0.179 (0.000%) 102: dt: 0.5000, sse=5033.3, rms=0.178 (0.000%) 103: dt: 0.5000, sse=4991.2, rms=0.177 (0.000%) 104: dt: 0.5000, sse=4932.2, rms=0.176 (0.000%) 105: dt: 0.5000, sse=4870.8, rms=0.174 (0.000%) 106: dt: 0.5000, sse=4849.9, rms=0.174 (0.000%) 107: dt: 0.5000, sse=4805.0, rms=0.173 (0.000%) 108: dt: 0.5000, sse=4768.1, rms=0.172 (0.000%) 109: dt: 0.5000, sse=4710.1, rms=0.171 (0.000%) 110: dt: 0.5000, sse=4653.6, rms=0.169 (0.000%) 111: dt: 0.5000, sse=4651.7, rms=0.169 (0.000%) 112: dt: 0.5000, sse=4613.7, rms=0.168 (0.000%) 113: dt: 0.5000, sse=4595.6, rms=0.168 (0.000%) 114: dt: 0.5000, sse=4579.3, rms=0.167 (0.000%) 115: dt: 0.5000, sse=4556.7, rms=0.167 (0.000%) 116: dt: 0.5000, sse=4543.0, rms=0.167 (0.000%) 117: dt: 0.5000, sse=4515.4, rms=0.166 (0.000%) 118: dt: 0.5000, sse=4500.7, rms=0.165 (0.000%) 119: dt: 0.5000, sse=4502.4, rms=0.165 (0.000%) 120: dt: 0.5000, sse=4468.9, rms=0.165 (0.000%) positioning took 2.4 minutes writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.area.pial vertex spacing 1.06 +- 0.45 (0.09-->7.00) (max @ vno 98589 --> 98572) face area 0.43 +- 0.31 (0.00-->8.30) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed 0 of 133935 vertices processed 25000 of 133935 vertices processed 50000 of 133935 vertices processed 75000 of 133935 vertices processed 100000 of 133935 vertices processed 125000 of 133935 vertices processed thickness calculation complete, 348:713 truncations. 67484 vertices at 0 distance 98737 vertices at 1 distance 60722 vertices at 2 distance 18863 vertices at 3 distance 5140 vertices at 4 distance 1510 vertices at 5 distance 521 vertices at 6 distance 190 vertices at 7 distance 64 vertices at 8 distance 42 vertices at 9 distance 24 vertices at 10 distance 22 vertices at 11 distance 14 vertices at 12 distance 18 vertices at 13 distance 9 vertices at 14 distance 6 vertices at 15 distance 3 vertices at 16 distance 3 vertices at 17 distance 4 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/lh.thickness positioning took 12.0 minutes /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/scripts mris_make_surfaces -orig_white white -orig_pial woFLAIR.pial -white NOWRITE -mgz -T1 brain.finalsurfs -FLAIR ../mri/FLAIR -nsigma_above 3 -nsigma_below 3 Andre_v_5_3 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... deforming surfaces based on FLAIR volume ../mri/FLAIR using T2 threshold of 3.00 sigmas above the mean (default=2) using T2 threshold of 3.00 sigmas below the mean (default=2) using white starting white location... using woFLAIR.pial starting pial locations... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/filled.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/brain.finalsurfs.mgz... reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/wm.mgz... 15222 bright wm thresholded. 275 bright non-wm voxels segmented. reading original surface position from /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/surf/rh.orig... computing class statistics... border white: 253146 voxels (1.51%) border gray 277015 voxels (1.65%) WM (92.0): 92.5 +- 9.5 [70.0 --> 110.0] GM (76.0) : 72.9 +- 14.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 40.7 (was 70) setting MAX_BORDER_WHITE to 111.5 (was 105) setting MIN_BORDER_WHITE to 55.0 (was 85) setting MAX_CSF to 26.5 (was 40) setting MAX_GRAY to 92.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 47.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 12.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=102, GM=55 mean inside = 90.3, mean outside = 67.5 smoothing surface for 5 iterations... reading initial white vertex positions from white... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /net/lagringshotell/psi-fmri/fmri/Projects/IVS_TEST/test_IVS_081014/Andre_v_5_3/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.92 +- 0.26 (0.01-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 7 points - only 0.00% unknown deleting segment 7 with 22 points - only 0.00% unknown deleting segment 8 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 9 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 2 points - only 0.00% unknown deleting segment 12 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 15 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=2.0, host=psyk-, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 001: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=1.0, host=psyk-, 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 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 002: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=0.5, host=psyk-, 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 0.92 +- 0.25 (0.08-->8.37) (max @ vno 72167 --> 134425) face area 0.35 +- 0.17 (0.00-->5.95) averaging target values for 5 iterations... 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 003: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 324 points - only 32.41% unknown deleting segment 1 with 7 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 3 with 4 points - only 0.00% unknown deleting segment 4 with 5 points - only 0.00% unknown deleting segment 5 with 7 points - only 0.00% unknown deleting segment 6 with 22 points - only 0.00% unknown deleting segment 7 with 363 points - only 9.64% unknown removing 4 vertex label from ripped group deleting segment 8 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 2 points - only 0.00% unknown deleting segment 10 with 71 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 11 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 12 with 1 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 13 with 1 points - only 0.00% unknown deleting segment 14 with 11 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown tol=1.0e-04, sigma=0.2, host=psyk-, 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 repositioning cortical surface to gray/csf boundary. HISTOalloc(-2147483648): could not allocate histogram 000: dt: 0.0000, sse=4063955.2, rms=0.00 rms = 1.91, time step reduction 1 of 3 to 0.250... rms = 0.49, time step reduction 2 of 3 to 0.125... rms = 0.06, time step reduction 3 of 3 to 0.062... 004: dt: 0.1250, sse=4063955.2, rms=0.000 (1.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 2 with 3 points - only 0.00% unknown smoothing surface for 5 iterations... reading initial pial vertex positions from woFLAIR.pial... repositioning pial surface locations using ../mri/FLAIR.mgz compressed histogram detected, changing bin size to 0.000000 Cannot allocate memory Linux psyk-stud140.uio.no 2.6.32-431.29.2.el6.x86_64 #1 SMP Sun Jul 27 15:55:46 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s Andre_v_5_3 exited with ERRORS at Tue Oct 14 17:13:52 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting