Fri Mar 30 18:24:55 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 /usr/local/freesurfer/dev/bin/recon-all -subject cvs_avg35_inMNI152 -no-isrunning -all -i cvs_avg35_inMNI152.mgz subjid cvs_avg35_inMNI152 setenv SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0_x86_64/dev build-stamp.txt: freesurfer-Linux-centos4_x86_64-dev-20120330 Linux compute-0-104.local 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 4096 memorylocked unlimited maxproc 268288 total used free shared buffers cached Mem: 32961676 4351772 28609904 0 433008 539508 -/+ buffers/cache: 3379256 29582420 Swap: 32764556 0 32764556 ######################################## program versions used $Id: recon-all,v 1.414 2012/03/21 20:43:24 mreuter 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: $ TimeStamp: 2012/03/30-22:24:57-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_convert.c,v 1.192 2012/03/21 20:54:29 mreuter Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version dev build (use --all-info flag for full version info) ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:01-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: tkregister2.c,v 1.126 2012/01/20 21:00:37 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 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: $ TimeStamp: 2012/03/30-22:25:05-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:06-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_normalize.c,v 1.79 2012/02/09 21:24:24 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:07-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_watershed.cpp,v 1.97 2011/11/08 22:17:40 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:07-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:08-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_segment.c,v 1.41 2011/08/04 19:39:41 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:08-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_label2label.c,v 1.41 2011/05/19 17:21:43 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:08-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_em_register.c,v 1.94 2011/10/25 13:53:06 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:10-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_ca_normalize.c,v 1.61 2012/03/01 18:49:31 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:10-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_ca_register.c,v 1.80 2012/03/17 20:44:41 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:11-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_ca_label.c,v 1.98 2012/02/21 21:04:20 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:12-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_pretess.c,v 1.21 2011/08/15 14:12:46 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:12-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:13-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:14-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:15-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:15-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:16-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_inflate.c,v 1.44 2012/01/05 18:36:17 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:17-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:17-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:18-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:18-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:19-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:21-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:22-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_make_surfaces.c,v 1.130 2011/12/08 15:01:24 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:23-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_register.c,v 1.60 2011/09/20 17:53:32 fischl Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:24-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:25-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:26-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:27-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:28-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mris_calc.c,v 1.47 2011/12/07 17:13:37 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.61 2012/03/06 19:54:03 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:30-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_robust_register.cpp,v 1.61 2012/03/06 19:54:03 mreuter Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.42 2012/03/29 20:08:02 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:30-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_robust_template.cpp,v 1.42 2012/03/29 20:08:02 mreuter Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:31-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:31-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_or.c,v 1.4 2011/10/06 21:08:23 lzollei Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:32-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2012/03/30-22:25:33-GMT BuildTimeStamp: Mar 30 2012 05:11:06 CVS: $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ User: lzollei Machine: compute-0-104.local Platform: Linux PlatformVersion: 2.6.18-308.1.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/dev/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/dev/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_convert /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig/001.mgz mri_convert /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig/001.mgz $Id: mri_convert.c,v 1.192 2012/03/21 20:54:29 mreuter Exp $ reading from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Mar 30 18:25:37 EDT 2012 Found 1 runs /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig/001.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_convert /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz -rt cubic --conform mri_convert /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz -rt cubic --conform $Id: mri_convert.c,v 1.192 2012/03/21 20:54:29 mreuter Exp $ reading from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/transforms/talairach.xfm /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Mar 30 18:25:44 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Fri Mar 30 18:28:19 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7228, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/dev/bin/extract_talairach_avi_QA.awk /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/transforms/talairach_avi.log TalAviQA: 0.96713 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Fri Mar 30 18:28:20 EDT 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri /usr/local/freesurfer/dev/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 2011/03/02 20:16:39 nicks Exp $ Linux compute-0-104.local 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux Fri Mar 30 18:28:20 EDT 2012 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.18948 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18948/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.18948/nu0.mnc -odt float $Id: mri_convert.c,v 1.192 2012/03/21 20:54:29 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.18948/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Mar 30 18:28:30 EDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.18948/nu0.mnc ./tmp.mri_nu_correct.mni.18948/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.18948/0/ [lzollei@compute-0-104.local:/autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/] [2012-03-30 18:28:30] running: /usr/local/freesurfer/dev/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.18948/0/ ./tmp.mri_nu_correct.mni.18948/nu0.mnc ./tmp.mri_nu_correct.mni.18948/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000960216 [lzollei@compute-0-104.local:/autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/] [2012-03-30 18:28:56] running: /usr/local/freesurfer/dev/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18948/nu0.mnc ./tmp.mri_nu_correct.mni.18948/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Mar 30 18:29:17 EDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.18948/nu1.mnc ./tmp.mri_nu_correct.mni.18948/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.18948/1/ [lzollei@compute-0-104.local:/autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/] [2012-03-30 18:29:17] running: /usr/local/freesurfer/dev/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.18948/1/ ./tmp.mri_nu_correct.mni.18948/nu1.mnc ./tmp.mri_nu_correct.mni.18948/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000969902 [lzollei@compute-0-104.local:/autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/] [2012-03-30 18:29:31] running: /usr/local/freesurfer/dev/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.18948/nu1.mnc ./tmp.mri_nu_correct.mni.18948/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.18948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18948/ones.mgz $Id: mri_binarize.c,v 1.34 2012/03/09 00:33:25 greve Exp $ cwd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.18948/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.18948/ones.mgz sysname Linux hostname compute-0-104.local machine x86_64 user lzollei input ./tmp.mri_nu_correct.mni.18948/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.18948/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18948/input.mean.dat $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18948/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.18948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18948/input.mean.dat sysname Linux hostname compute-0-104.local machine x86_64 user lzollei Loading ./tmp.mri_nu_correct.mni.18948/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.18948/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18948/ones.mgz --i ./tmp.mri_nu_correct.mni.18948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18948/output.mean.dat $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.18948/ones.mgz --i ./tmp.mri_nu_correct.mni.18948/nu2.mnc --sum ./tmp.mri_nu_correct.mni.18948/sum.junk --avgwf ./tmp.mri_nu_correct.mni.18948/output.mean.dat sysname Linux hostname compute-0-104.local machine x86_64 user lzollei Loading ./tmp.mri_nu_correct.mni.18948/ones.mgz Loading ./tmp.mri_nu_correct.mni.18948/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.18948/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.18948/nu2.mnc ./tmp.mri_nu_correct.mni.18948/nu2.mnc mul .90362274092371119364 Saving result to './tmp.mri_nu_correct.mni.18948/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.18948/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.18948/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.192 2012/03/21 20:54:29 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.18948/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 12 seconds. mapping (16, 104) to ( 3, 110) Fri Mar 30 18:31:16 EDT 2012 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Fri Mar 30 18:31:16 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.054 0.003 -0.007 -0.076; -0.011 1.091 0.009 1.779; 0.020 -0.060 1.101 -5.461; 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 = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 84 (84), valley at 73 (73) csf peak at 54, setting threshold to 74 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 109 gm peak at 87 (87), valley at 76 (76) csf peak at 57, setting threshold to 77 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 17 seconds. #-------------------------------------------- #@# Skull Stripping Fri Mar 30 18:33:35 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 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/dev/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=23.0 skull bounding box = (55, 69, 43) --> (196, 197, 213) using (102, 112, 128) as brain centroid... mean wm in atlas = 126, using box (85,96,107) --> (119, 127,148) to find MRI wm before smoothing, mri peak at 112 after smoothing, mri peak at 111, scaling input intensities by 1.135 scaling channel 0 by 1.13514 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.627439 @ (9.091, -9.091, -9.091) max log p = -4.311954 @ (-13.636, -13.636, -13.636) max log p = -4.071712 @ (2.273, 2.273, 2.273) max log p = -4.066154 @ (1.136, 1.136, 1.136) max log p = -4.066154 @ (0.000, 0.000, 0.000) max log p = -4.066154 @ (0.000, 0.000, 0.000) Found translation: (-1.1, -19.3, -19.3): log p = -4.066 **************************************** Nine parameter search. iteration 0 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 -9.226; 0.000 1.236 0.000 -52.495; 0.000 0.000 1.075 -28.720; 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) 1.144 0.000 0.000 -19.350; 0.000 1.236 0.000 -52.495; 0.000 0.000 1.156 -38.826; 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) 1.144 0.000 0.000 -19.350; 0.000 1.236 0.000 -52.495; 0.000 0.000 1.156 -38.826; 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=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.121 0.000 0.000 -16.527; 0.000 1.167 0.036 -45.485; 0.000 -0.038 1.091 -27.145; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.121 0.000 0.000 -16.527; 0.000 1.167 0.036 -45.485; 0.000 -0.038 1.091 -27.145; 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.120 -0.000 0.000 -16.321; 0.000 1.171 0.036 -46.110; 0.000 -0.038 1.095 -27.150; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.120 -0.000 0.000 -16.321; 0.000 1.170 0.018 -43.709; 0.000 -0.019 1.099 -29.871; 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 1.11997 -0.00031 0.00003 -16.32141; 0.00030 1.17016 0.01786 -43.70948; 0.00005 -0.01928 1.09898 -29.87095; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.11997 -0.00031 0.00003 -16.32141; 0.00030 1.17016 0.01786 -43.70948; 0.00005 -0.01928 1.09898 -29.87095; 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: 1.120 -0.000 0.000 -16.321; 0.000 1.170 0.018 -43.709; 0.000 -0.019 1.099 -29.871; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.8) transform before final EM align: 1.120 -0.000 0.000 -16.321; 0.000 1.170 0.018 -43.709; 0.000 -0.019 1.099 -29.871; 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 1.11997 -0.00031 0.00003 -16.32141; 0.00030 1.17016 0.01786 -43.70948; 0.00005 -0.01928 1.09898 -29.87095; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.11997 -0.00031 0.00003 -16.32141; 0.00030 1.17016 0.01786 -43.70948; 0.00005 -0.01928 1.09898 -29.87095; 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) = 4.4 tol 0.000000 final transform: 1.120 -0.000 0.000 -16.321; 0.000 1.170 0.018 -43.709; 0.000 -0.019 1.099 -29.871; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 28 minutes and 52 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/dev/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=128 y=123 z=136 r=64 first estimation of the main basin volume: 1121899 voxels Looking for seedpoints 2 found in the cerebellum 14 found in the rest of the brain global maximum in x=150, y=110, z=106, Imax=255 CSF=11, 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=17686403726 voxels, voxel volume =1.000 = 17686403726 mmm3 = 17686403.072 cm3 done. PostAnalyze...Basin Prior 1 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=137, z=123, r=9652 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 46098 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3330 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 2718 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19836 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 19692 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 522 (2) Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 3, 23, 50 after analyzing : 3, 17, 25, 25 RIGHT_CER before analyzing : 3, 3, 23, 50 after analyzing : 3, 17, 25, 25 LEFT_CER before analyzing : 3, 3, 23, 50 after analyzing : 3, 17, 25, 25 RIGHT_BRAIN before analyzing : 3, 3, 23, 48 after analyzing : 3, 17, 25, 24 LEFT_BRAIN before analyzing : 3, 3, 23, 50 after analyzing : 3, 17, 25, 25 OTHER before analyzing : 3, 3, 10, 49 after analyzing : 3, 17, 25, 25 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...72 iterations *********************VALIDATION********************* curvature mean = -0.011, std = 0.010 curvature mean = 76.382, std = 7.623 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.31, sigma = 5.39 after rotation: sse = 3.31, sigma = 5.39 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.52, its var is 4.95 before Erosion-Dilatation 0.62% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...38 iterations mri_strip_skull: done peeling brain Brain Size = 2151789 voxels, voxel volume = 1.000 mm3 = 2151789 mmm3 = 2151.789 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Mar 30 19:03:03 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca transforms/talairach.lta 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/dev/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=23.0 skull bounding box = (55, 69, 43) --> (196, 197, 213) using (102, 112, 128) as brain centroid... mean wm in atlas = 107, using box (85,96,107) --> (119, 127,148) to find MRI wm before smoothing, mri peak at 112 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.089640 @ (-9.091, -9.091, -9.091) max log p = -3.591251 @ (4.545, -13.636, -13.636) max log p = -2.998065 @ (2.273, 2.273, 2.273) max log p = -2.928880 @ (1.136, 1.136, 1.136) max log p = -2.928880 @ (0.000, 0.000, 0.000) max log p = -2.928880 @ (0.000, 0.000, 0.000) Found translation: (-1.1, -19.3, -19.3): log p = -2.929 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-2.9, old_max_log_p =-2.9 (thresh=-2.9) 1.000 0.000 0.000 -1.136; 0.000 1.000 0.000 -19.318; 0.000 0.000 1.000 -19.318; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-2.9, old_max_log_p =-2.9 (thresh=-2.9) 1.000 0.000 0.000 -1.136; 0.000 1.018 0.000 -21.812; 0.000 0.000 1.000 -19.318; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-2.9, old_max_log_p =-2.9 (thresh=-2.9) 1.000 0.000 0.000 -1.136; 0.000 1.018 0.000 -21.812; 0.000 0.000 1.000 -19.318; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-2.9, old_max_log_p =-2.9 (thresh=-2.9) 0.996 -0.017 0.000 1.590; 0.016 1.021 -0.008 -23.356; -0.000 0.008 0.996 -19.532; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-2.9, old_max_log_p =-2.9 (thresh=-2.9) 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 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 0.99635 -0.01660 0.00027 1.59021; 0.01644 1.02265 -0.00826 -23.52270; -0.00013 0.00825 0.99528 -19.38529; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.99635 -0.01660 0.00027 1.59021; 0.01644 1.02265 -0.00826 -23.52270; -0.00013 0.00825 0.99528 -19.38529; 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: 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -2.9 (old=-4.3) transform before final EM align: 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 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 0.99635 -0.01660 0.00027 1.59021; 0.01644 1.02265 -0.00826 -23.52270; -0.00013 0.00825 0.99528 -19.38529; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.99635 -0.01660 0.00027 1.59021; 0.01644 1.02265 -0.00826 -23.52270; -0.00013 0.00825 0.99528 -19.38529; 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) = 3.4 tol 0.000000 final transform: 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 16 minutes and 24 seconds. #-------------------------------------- #@# CA Normalize Fri Mar 30 19:19:27 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/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/dev/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=23.0 skull bounding box = (55, 69, 43) --> (196, 197, 213) using (102, 112, 128) as brain centroid... mean wm in atlas = 107, using box (85,96,107) --> (119, 127,148) to find MRI wm before smoothing, mri peak at 112 after smoothing, mri peak at 111, scaling input intensities by 0.964 scaling channel 0 by 0.963964 using 244171 sample points... INFO: compute sample coordinates transform 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 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 (125, 72, 44) --> (194, 188, 213) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 119.0 4 of 5739 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 44) --> (127, 189, 213) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 119.0 4 of 5752 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 153, 66) --> (178, 196, 121) Left_Cerebellum_White_Matter: limiting intensities to 77.0 --> 119.0 0 of 509 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 153, 64) --> (128, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 75.0 --> 119.0 0 of 469 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 149, 100) --> (144, 215, 133) Brain_Stem: limiting intensities to 72.0 --> 119.0 0 of 938 (0.0%) samples deleted using 13407 total control points for intensity normalization... bias field = 1.013 +- 0.038 3 of 13399 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 72, 44) --> (194, 188, 213) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 120.0 1 of 5847 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 44) --> (127, 189, 213) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 120.0 0 of 5902 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 153, 66) --> (178, 196, 121) Left_Cerebellum_White_Matter: limiting intensities to 79.0 --> 120.0 0 of 498 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 153, 64) --> (128, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 77.0 --> 120.0 0 of 464 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 149, 100) --> (144, 215, 133) Brain_Stem: limiting intensities to 72.0 --> 120.0 0 of 921 (0.0%) samples deleted using 13632 total control points for intensity normalization... bias field = 1.021 +- 0.026 15 of 13631 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (125, 72, 44) --> (194, 188, 213) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 121.0 2 of 5801 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 44) --> (127, 189, 213) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 121.0 0 of 5866 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 153, 66) --> (178, 196, 121) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 121.0 0 of 484 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (82, 153, 64) --> (128, 196, 121) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 121.0 0 of 456 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (111, 149, 100) --> (144, 215, 133) Brain_Stem: limiting intensities to 72.0 --> 121.0 0 of 914 (0.0%) samples deleted using 13521 total control points for intensity normalization... bias field = 1.019 +- 0.023 13 of 13519 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 48 seconds. #-------------------------------------- #@# CA Reg Fri Mar 30 19:21:16 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/dev/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 reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.01 (predicted orig area = 7.9) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 0001: dt=129.472000, rms=0.595 (7.580%), neg=0, invalid=766 0002: dt=129.472000, rms=0.578 (2.759%), neg=0, invalid=766 0003: dt=129.472000, rms=0.574 (0.826%), neg=0, invalid=766 0004: dt=129.472000, rms=0.564 (1.622%), neg=0, invalid=766 0005: dt=55.488000, rms=0.563 (0.162%), neg=0, invalid=766 0006: dt=55.488000, rms=0.562 (0.307%), neg=0, invalid=766 0007: dt=55.488000, rms=0.559 (0.532%), neg=0, invalid=766 0008: dt=55.488000, rms=0.555 (0.670%), neg=0, invalid=766 0009: dt=55.488000, rms=0.551 (0.731%), neg=0, invalid=766 0010: dt=55.488000, rms=0.547 (0.708%), neg=0, invalid=766 0011: dt=55.488000, rms=0.544 (0.603%), neg=0, invalid=766 0012: dt=55.488000, rms=0.541 (0.476%), neg=0, invalid=766 0013: dt=55.488000, rms=0.539 (0.385%), neg=0, invalid=766 0014: dt=55.488000, rms=0.537 (0.345%), neg=0, invalid=766 0015: dt=55.488000, rms=0.535 (0.356%), neg=0, invalid=766 0016: dt=55.488000, rms=0.533 (0.353%), neg=0, invalid=766 0017: dt=55.488000, rms=0.532 (0.323%), neg=0, invalid=766 0018: dt=55.488000, rms=0.530 (0.286%), neg=0, invalid=766 0019: dt=55.488000, rms=0.529 (0.259%), neg=0, invalid=766 0020: dt=55.488000, rms=0.527 (0.261%), neg=0, invalid=766 0021: dt=55.488000, rms=0.526 (0.242%), neg=0, invalid=766 0022: dt=55.488000, rms=0.525 (0.203%), neg=0, invalid=766 0023: dt=55.488000, rms=0.524 (0.164%), neg=0, invalid=766 0024: dt=55.488000, rms=0.523 (0.144%), neg=0, invalid=766 0025: dt=55.488000, rms=0.523 (0.150%), neg=0, invalid=766 0026: dt=55.488000, rms=0.522 (0.158%), neg=0, invalid=766 0027: dt=55.488000, rms=0.521 (0.180%), neg=0, invalid=766 0028: dt=55.488000, rms=0.520 (0.175%), neg=0, invalid=766 0029: dt=55.488000, rms=0.519 (0.171%), neg=0, invalid=766 0030: dt=55.488000, rms=0.518 (0.168%), neg=0, invalid=766 0031: dt=55.488000, rms=0.517 (0.142%), neg=0, invalid=766 0032: dt=55.488000, rms=0.517 (0.143%), neg=0, invalid=766 0033: dt=55.488000, rms=0.516 (0.142%), neg=0, invalid=766 0034: dt=55.488000, rms=0.515 (0.137%), neg=0, invalid=766 0035: dt=55.488000, rms=0.515 (0.127%), neg=0, invalid=766 0036: dt=55.488000, rms=0.514 (0.123%), neg=0, invalid=766 0037: dt=55.488000, rms=0.513 (0.109%), neg=0, invalid=766 0038: dt=1183.744000, rms=0.512 (0.188%), neg=0, invalid=766 0039: dt=129.472000, rms=0.512 (0.065%), neg=0, invalid=766 0040: dt=129.472000, rms=0.512 (0.015%), neg=0, invalid=766 0041: dt=129.472000, rms=0.512 (0.035%), neg=0, invalid=766 0042: dt=129.472000, rms=0.511 (0.079%), neg=0, invalid=766 0043: dt=129.472000, rms=0.511 (0.075%), neg=0, invalid=766 0044: dt=129.472000, rms=0.511 (0.094%), neg=0, invalid=766 0045: dt=129.472000, rms=0.510 (0.102%), neg=0, invalid=766 0046: dt=129.472000, rms=0.510 (0.109%), neg=0, invalid=766 0047: dt=129.472000, rms=0.509 (0.106%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=766 0048: dt=32.368000, rms=0.509 (0.006%), neg=0, invalid=766 0049: dt=73.984000, rms=0.509 (0.017%), neg=0, invalid=766 0050: dt=517.888000, rms=0.508 (0.150%), neg=0, invalid=766 0051: dt=8.092000, rms=0.508 (-0.007%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=766 0052: dt=145.152000, rms=0.501 (2.436%), neg=0, invalid=766 0053: dt=82.944000, rms=0.490 (2.081%), neg=0, invalid=766 0054: dt=15.552000, rms=0.489 (0.321%), neg=0, invalid=766 0055: dt=36.288000, rms=0.487 (0.362%), neg=0, invalid=766 0056: dt=145.152000, rms=0.479 (1.612%), neg=0, invalid=766 0057: dt=9.072000, rms=0.478 (0.169%), neg=0, invalid=766 0058: dt=9.072000, rms=0.478 (0.099%), neg=0, invalid=766 0059: dt=9.072000, rms=0.478 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.478, neg=0, invalid=766 0060: dt=20.736000, rms=0.477 (0.078%), neg=0, invalid=766 0061: dt=248.832000, rms=0.470 (1.558%), neg=0, invalid=766 0062: dt=9.072000, rms=0.469 (0.057%), neg=0, invalid=766 0063: dt=9.072000, rms=0.469 (0.087%), neg=0, invalid=766 0064: dt=9.072000, rms=0.469 (0.068%), neg=0, invalid=766 0065: dt=9.072000, rms=0.468 (0.069%), neg=0, invalid=766 0066: dt=9.072000, rms=0.468 (0.098%), neg=0, invalid=766 0067: dt=9.072000, rms=0.467 (0.179%), neg=0, invalid=766 0068: dt=9.072000, rms=0.466 (0.239%), neg=0, invalid=766 0069: dt=9.072000, rms=0.465 (0.258%), neg=0, invalid=766 0070: dt=9.072000, rms=0.464 (0.239%), neg=0, invalid=766 0071: dt=9.072000, rms=0.463 (0.205%), neg=0, invalid=766 0072: dt=9.072000, rms=0.462 (0.163%), neg=0, invalid=766 0073: dt=9.072000, rms=0.461 (0.131%), neg=0, invalid=766 0074: dt=9.072000, rms=0.461 (0.108%), neg=0, invalid=766 0075: dt=9.072000, rms=0.460 (0.129%), neg=0, invalid=766 0076: dt=9.072000, rms=0.459 (0.180%), neg=0, invalid=766 0077: dt=9.072000, rms=0.458 (0.222%), neg=0, invalid=766 0078: dt=9.072000, rms=0.457 (0.217%), neg=0, invalid=766 0079: dt=9.072000, rms=0.457 (0.200%), neg=0, invalid=766 0080: dt=9.072000, rms=0.456 (0.173%), neg=0, invalid=766 0081: dt=9.072000, rms=0.455 (0.140%), neg=0, invalid=766 0082: dt=9.072000, rms=0.455 (0.116%), neg=0, invalid=766 0083: dt=9.072000, rms=0.454 (0.095%), neg=0, invalid=766 0084: dt=145.152000, rms=0.453 (0.177%), neg=0, invalid=766 0085: dt=9.072000, rms=0.453 (0.008%), neg=0, invalid=766 0086: dt=9.072000, rms=0.453 (0.007%), neg=0, invalid=766 0087: dt=9.072000, rms=0.453 (-0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.472, neg=0, invalid=766 0088: dt=11.200000, rms=0.471 (0.231%), neg=0, invalid=766 0089: dt=11.200000, rms=0.470 (0.081%), neg=0, invalid=766 0090: dt=11.200000, rms=0.470 (0.054%), neg=0, invalid=766 0091: dt=11.200000, rms=0.470 (-0.109%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 0092: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=766 0093: dt=3.687500, rms=0.508 (0.648%), neg=0, invalid=766 0094: dt=0.720000, rms=0.508 (0.009%), neg=0, invalid=766 0095: dt=0.720000, rms=0.508 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.508, neg=0, invalid=766 0096: dt=0.144000, rms=0.508 (0.001%), neg=0, invalid=766 0097: dt=0.045000, rms=0.508 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.566, neg=0, invalid=766 0098: dt=1.536000, rms=0.559 (1.189%), neg=0, invalid=766 0099: dt=1.792000, rms=0.556 (0.570%), neg=0, invalid=766 0100: dt=0.768000, rms=0.555 (0.200%), neg=0, invalid=766 0101: dt=0.768000, rms=0.555 (0.028%), neg=0, invalid=766 0102: dt=0.768000, rms=0.555 (-0.043%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.555, neg=0, invalid=766 0103: dt=1.280000, rms=0.554 (0.088%), neg=0, invalid=766 0104: dt=0.000000, rms=0.554 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.513, neg=0, invalid=766 0105: dt=0.320000, rms=0.506 (1.400%), neg=0, invalid=766 0106: dt=0.000000, rms=0.506 (0.014%), neg=0, invalid=766 0107: dt=0.050000, rms=0.506 (-0.088%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.506, neg=0, invalid=766 0108: dt=0.001250, rms=0.506 (0.000%), neg=0, invalid=766 0109: dt=0.000000, rms=0.506 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.08817 ( 3) Left_Lateral_Ventricle (4): linear fit = 0.08 x + 0.0 (2191 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2191 voxels, peak = 2), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.10958 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.08 x + 0.0 (1931 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1931 voxels, peak = 2), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.10490 (91) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (752 voxels, overlap=0.009) Right_Pallidum (52): linear fit = 0.90 x + 0.0 (752 voxels, peak = 90), gca=90.0 gca peak = 0.19192 (97) mri peak = 0.11177 (88) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (673 voxels, overlap=0.025) Left_Pallidum (13): linear fit = 0.90 x + 0.0 (673 voxels, peak = 87), gca=87.3 gca peak = 0.24007 (63) mri peak = 0.20144 (50) Right_Hippocampus (53): linear fit = 0.77 x + 0.0 (1456 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 0.77 x + 0.0 (1456 voxels, peak = 49), gca=48.8 gca peak = 0.29892 (64) mri peak = 0.11489 (53) Left_Hippocampus (17): linear fit = 0.80 x + 0.0 (1584 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 0.80 x + 0.0 (1584 voxels, peak = 51), gca=51.2 gca peak = 0.12541 (104) mri peak = 0.09193 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (115033 voxels, overlap=0.859) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (115033 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.09203 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (117623 voxels, overlap=0.824) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (117623 voxels, peak = 104), gca=104.0 gca peak = 0.11691 (63) mri peak = 0.04440 (51) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (78198 voxels, overlap=0.119) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (78198 voxels, peak = 52), gca=52.0 gca peak = 0.13270 (63) mri peak = 0.04398 (51) Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (77650 voxels, overlap=0.014) Right_Cerebral_Cortex (42): linear fit = 0.77 x + 0.0 (77650 voxels, peak = 49), gca=48.8 gca peak = 0.15182 (70) mri peak = 0.10119 (53) Right_Caudate (50): linear fit = 0.77 x + 0.0 (1030 voxels, overlap=0.002) Right_Caudate (50): linear fit = 0.77 x + 0.0 (1030 voxels, peak = 54), gca=54.2 gca peak = 0.14251 (76) mri peak = 0.07327 (68) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1336 voxels, overlap=0.250) Left_Caudate (11): linear fit = 0.85 x + 0.0 (1336 voxels, peak = 65), gca=64.6 gca peak = 0.12116 (60) mri peak = 0.05425 (60) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (47485 voxels, overlap=0.947) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (47485 voxels, peak = 60), gca=60.0 gca peak = 0.12723 (61) mri peak = 0.05781 (58) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (52000 voxels, overlap=0.979) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (52000 voxels, peak = 61), gca=61.0 gca peak = 0.22684 (88) mri peak = 0.10120 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (13914 voxels, overlap=0.948) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (13914 voxels, peak = 90), gca=90.2 gca peak = 0.21067 (87) mri peak = 0.10365 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (12289 voxels, overlap=0.964) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (12289 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.20594 (51) Left_Amygdala: unreasonable value (49.6/51.0), not in range [50, 90] - rejecting gca peak = 0.39668 (62) mri peak = 0.36556 (50) Right_Amygdala: unreasonable value (49.6/50.0), not in range [50, 90] - rejecting gca peak = 0.10129 (93) mri peak = 0.08782 (84) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (6988 voxels, overlap=0.489) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (6988 voxels, peak = 84), gca=83.7 gca peak = 0.12071 (89) mri peak = 0.10938 (76) Right_Thalamus_Proper (49): linear fit = 0.90 x + 0.0 (6472 voxels, overlap=0.304) Right_Thalamus_Proper (49): linear fit = 0.90 x + 0.0 (6472 voxels, peak = 80), gca=80.1 gca peak = 0.13716 (82) mri peak = 0.06151 (72) Left_Putamen (12): linear fit = 0.85 x + 0.0 (3744 voxels, overlap=0.545) Left_Putamen (12): linear fit = 0.85 x + 0.0 (3744 voxels, peak = 70), gca=69.7 gca peak = 0.15214 (84) mri peak = 0.06640 (66) Right_Putamen (51): linear fit = 0.82 x + 0.0 (3832 voxels, overlap=0.429) Right_Putamen (51): linear fit = 0.82 x + 0.0 (3832 voxels, peak = 69), gca=69.3 gca peak = 0.08983 (85) mri peak = 0.10029 (86) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17671 voxels, overlap=0.774) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17671 voxels, peak = 85), gca=85.0 gca peak = 0.11809 (92) mri peak = 0.07855 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1641 voxels, overlap=0.852) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1641 voxels, peak = 92), gca=92.0 gca peak = 0.12914 (94) mri peak = 0.08603 (96) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2145 voxels, overlap=0.840) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2145 voxels, peak = 92), gca=91.7 gca peak = 0.21100 (36) mri peak = 0.11112 (39) gca peak = 0.13542 (27) mri peak = 0.14036 ( 2) Fourth_Ventricle (15): linear fit = 0.08 x + 0.0 (316 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.08 x + 0.0 (316 voxels, peak = 2), gca=2.0 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 Left_Amygdala = 0.25455 (62) 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_Amygdala = 0.39668 (62) 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) not using caudate to estimate GM means estimating mean gm scale to be 0.79 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=766 0110: dt=129.472000, rms=0.520 (1.378%), neg=0, invalid=766 0111: dt=129.472000, rms=0.514 (1.038%), neg=0, invalid=766 0112: dt=32.368000, rms=0.513 (0.239%), neg=0, invalid=766 0113: dt=73.984000, rms=0.512 (0.156%), neg=0, invalid=766 0114: dt=443.904000, rms=0.507 (0.943%), neg=0, invalid=766 0115: dt=32.368000, rms=0.506 (0.207%), neg=0, invalid=766 0116: dt=23.120000, rms=0.506 (0.028%), neg=0, invalid=766 0117: dt=23.120000, rms=0.506 (0.009%), neg=0, invalid=766 0118: dt=23.120000, rms=0.506 (0.005%), neg=0, invalid=766 0119: dt=23.120000, rms=0.506 (0.021%), neg=0, invalid=766 0120: dt=23.120000, rms=0.506 (0.062%), neg=0, invalid=766 0121: dt=23.120000, rms=0.505 (0.118%), neg=0, invalid=766 0122: dt=23.120000, rms=0.504 (0.151%), neg=0, invalid=766 0123: dt=23.120000, rms=0.504 (0.147%), neg=0, invalid=766 0124: dt=23.120000, rms=0.503 (0.127%), neg=0, invalid=766 0125: dt=23.120000, rms=0.502 (0.110%), neg=0, invalid=766 0126: dt=23.120000, rms=0.502 (0.088%), neg=0, invalid=766 0127: dt=23.120000, rms=0.502 (0.074%), neg=0, invalid=766 0128: dt=23.120000, rms=0.501 (0.068%), neg=0, invalid=766 0129: dt=23.120000, rms=0.501 (0.082%), neg=0, invalid=766 0130: dt=23.120000, rms=0.500 (0.106%), neg=0, invalid=766 0131: dt=23.120000, rms=0.500 (0.114%), neg=0, invalid=766 0132: dt=23.120000, rms=0.499 (0.110%), neg=0, invalid=766 0133: dt=23.120000, rms=0.499 (0.096%), neg=0, invalid=766 0134: dt=23.120000, rms=0.498 (0.088%), neg=0, invalid=766 0135: dt=23.120000, rms=0.498 (0.066%), neg=0, invalid=766 0136: dt=23.120000, rms=0.498 (0.053%), neg=0, invalid=766 0137: dt=23.120000, rms=0.497 (0.051%), neg=0, invalid=766 0138: dt=23.120000, rms=0.497 (0.061%), neg=0, invalid=766 0139: dt=23.120000, rms=0.497 (0.073%), neg=0, invalid=766 0140: dt=23.120000, rms=0.496 (0.076%), neg=0, invalid=766 0141: dt=23.120000, rms=0.496 (0.072%), neg=0, invalid=766 0142: dt=23.120000, rms=0.496 (0.070%), neg=0, invalid=766 0143: dt=23.120000, rms=0.495 (0.059%), neg=0, invalid=766 0144: dt=23.120000, rms=0.495 (0.049%), neg=0, invalid=766 0145: dt=23.120000, rms=0.495 (0.046%), neg=0, invalid=766 0146: dt=23.120000, rms=0.495 (0.046%), neg=0, invalid=766 0147: dt=23.120000, rms=0.494 (0.042%), neg=0, invalid=766 0148: dt=23.120000, rms=0.494 (0.053%), neg=0, invalid=766 0149: dt=23.120000, rms=0.494 (0.055%), neg=0, invalid=766 0150: dt=23.120000, rms=0.494 (0.056%), neg=0, invalid=766 0151: dt=23.120000, rms=0.493 (0.057%), neg=0, invalid=766 0152: dt=23.120000, rms=0.493 (0.046%), neg=0, invalid=766 0153: dt=23.120000, rms=0.493 (0.035%), neg=0, invalid=766 0154: dt=23.120000, rms=0.493 (0.034%), neg=0, invalid=766 0155: dt=23.120000, rms=0.493 (0.033%), neg=0, invalid=766 0156: dt=23.120000, rms=0.492 (0.035%), neg=0, invalid=766 0157: dt=23.120000, rms=0.492 (0.042%), neg=0, invalid=766 0158: dt=23.120000, rms=0.492 (0.040%), neg=0, invalid=766 0159: dt=23.120000, rms=0.492 (0.042%), neg=0, invalid=766 0160: dt=23.120000, rms=0.492 (0.038%), neg=0, invalid=766 0161: dt=23.120000, rms=0.492 (0.034%), neg=0, invalid=766 0162: dt=23.120000, rms=0.491 (0.030%), neg=0, invalid=766 0163: dt=23.120000, rms=0.491 (0.030%), neg=0, invalid=766 0164: dt=23.120000, rms=0.491 (0.028%), neg=0, invalid=766 0165: dt=23.120000, rms=0.491 (0.027%), neg=0, invalid=766 0166: dt=23.120000, rms=0.491 (0.033%), neg=0, invalid=766 0167: dt=23.120000, rms=0.491 (0.035%), neg=0, invalid=766 0168: dt=23.120000, rms=0.490 (0.034%), neg=0, invalid=766 0169: dt=23.120000, rms=0.490 (0.033%), neg=0, invalid=766 0170: dt=23.120000, rms=0.490 (0.029%), neg=0, invalid=766 0171: dt=23.120000, rms=0.490 (0.028%), neg=0, invalid=766 0172: dt=23.120000, rms=0.490 (0.026%), neg=0, invalid=766 0173: dt=23.120000, rms=0.490 (0.027%), neg=0, invalid=766 0174: dt=23.120000, rms=0.490 (0.027%), neg=0, invalid=766 0175: dt=23.120000, rms=0.489 (0.029%), neg=0, invalid=766 0176: dt=23.120000, rms=0.489 (0.029%), neg=0, invalid=766 0177: dt=23.120000, rms=0.489 (0.026%), neg=0, invalid=766 0178: dt=23.120000, rms=0.489 (0.024%), neg=0, invalid=766 0179: dt=23.120000, rms=0.489 (0.021%), neg=0, invalid=766 0180: dt=1479.680000, rms=0.489 (0.069%), neg=0, invalid=766 0181: dt=92.480000, rms=0.488 (0.088%), neg=0, invalid=766 0182: dt=0.000000, rms=0.488 (0.000%), neg=0, invalid=766 0183: dt=0.850000, rms=0.488 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=766 0184: dt=73.984000, rms=0.488 (0.020%), neg=0, invalid=766 0185: dt=443.904000, rms=0.488 (0.099%), neg=0, invalid=766 0186: dt=23.120000, rms=0.488 (0.005%), neg=0, invalid=766 0187: dt=23.120000, rms=0.488 (0.003%), neg=0, invalid=766 0188: dt=23.120000, rms=0.488 (0.002%), neg=0, invalid=766 0189: dt=23.120000, rms=0.488 (0.002%), neg=0, invalid=766 0190: dt=295.936000, rms=0.487 (0.088%), neg=0, invalid=766 0191: dt=13.872000, rms=0.487 (0.009%), neg=0, invalid=766 0192: dt=13.872000, rms=0.487 (-0.005%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.487, neg=0, invalid=766 0193: dt=36.288000, rms=0.484 (0.644%), neg=0, invalid=766 0194: dt=248.832000, rms=0.471 (2.684%), neg=0, invalid=766 0195: dt=9.072000, rms=0.469 (0.532%), neg=0, invalid=766 0196: dt=1.620000, rms=0.468 (0.120%), neg=0, invalid=766 0197: dt=0.141750, rms=0.468 (0.010%), neg=0, invalid=766 0198: dt=0.070875, rms=0.468 (0.002%), neg=0, invalid=766 0199: dt=0.035437, rms=0.468 (0.001%), neg=0, invalid=766 0200: dt=0.004430, rms=0.468 (0.000%), neg=0, invalid=766 0201: dt=0.002215, rms=0.468 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.468, neg=0, invalid=766 0202: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=766 0203: dt=0.000000, rms=0.468 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 0204: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=766 0205: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.475, neg=0, invalid=766 0206: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.475, neg=0, invalid=766 0207: dt=0.000000, rms=0.475 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.486, neg=0, invalid=766 0208: dt=0.448000, rms=0.483 (0.753%), neg=0, invalid=766 0209: dt=0.448000, rms=0.479 (0.680%), neg=0, invalid=766 0210: dt=0.448000, rms=0.476 (0.584%), neg=0, invalid=766 0211: dt=1.792000, rms=0.467 (1.954%), neg=0, invalid=766 0212: dt=1.792000, rms=0.462 (1.127%), neg=0, invalid=766 0213: dt=1.792000, rms=0.459 (0.652%), neg=0, invalid=766 0214: dt=1.792000, rms=0.457 (0.448%), neg=0, invalid=766 0215: dt=1.792000, rms=0.455 (0.310%), neg=0, invalid=766 0216: dt=7.168000, rms=0.451 (0.868%), neg=0, invalid=766 0217: dt=0.448000, rms=0.451 (0.001%), neg=0, invalid=766 0218: dt=0.448000, rms=0.451 (0.018%), neg=0, invalid=766 0219: dt=0.448000, rms=0.451 (0.012%), neg=0, invalid=766 0220: dt=0.448000, rms=0.451 (0.015%), neg=0, invalid=766 0221: dt=0.448000, rms=0.451 (0.028%), neg=0, invalid=766 0222: dt=0.448000, rms=0.451 (0.045%), neg=0, invalid=766 0223: dt=0.448000, rms=0.451 (0.051%), neg=0, invalid=766 0224: dt=0.448000, rms=0.450 (0.056%), neg=0, invalid=766 0225: dt=0.448000, rms=0.450 (0.045%), neg=0, invalid=766 0226: dt=0.448000, rms=0.450 (0.052%), neg=0, invalid=766 0227: dt=0.448000, rms=0.450 (0.046%), neg=0, invalid=766 0228: dt=0.448000, rms=0.450 (0.032%), neg=0, invalid=766 0229: dt=0.448000, rms=0.449 (0.027%), neg=0, invalid=766 0230: dt=0.448000, rms=0.449 (0.032%), neg=0, invalid=766 0231: dt=0.448000, rms=0.449 (0.016%), neg=0, invalid=766 0232: dt=0.448000, rms=0.449 (0.009%), neg=0, invalid=766 0233: dt=4.096000, rms=0.449 (0.019%), neg=0, invalid=766 0234: dt=0.768000, rms=0.449 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.449, neg=0, invalid=766 0235: dt=1.792000, rms=0.448 (0.162%), neg=0, invalid=766 0236: dt=7.375000, rms=0.447 (0.308%), neg=0, invalid=766 0237: dt=0.448000, rms=0.447 (-0.008%), neg=0, invalid=766 0238: dt=0.448000, rms=0.447 (0.005%), neg=0, invalid=766 0239: dt=0.448000, rms=0.447 (0.003%), neg=0, invalid=766 0240: dt=0.448000, rms=0.447 (-0.048%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.437, neg=0, invalid=766 0241: dt=0.112000, rms=0.434 (0.624%), neg=0, invalid=766 0242: dt=0.112000, rms=0.432 (0.495%), neg=0, invalid=766 0243: dt=0.112000, rms=0.430 (0.399%), neg=0, invalid=766 0244: dt=0.448000, rms=0.425 (1.256%), neg=0, invalid=766 0245: dt=0.096000, rms=0.425 (0.099%), neg=0, invalid=766 0246: dt=0.320000, rms=0.423 (0.297%), neg=0, invalid=766 0247: dt=0.028000, rms=0.423 (0.013%), neg=0, invalid=766 0248: dt=0.028000, rms=0.423 (0.018%), neg=0, invalid=766 0249: dt=0.028000, rms=0.423 (0.041%), neg=0, invalid=766 0250: dt=0.028000, rms=0.423 (0.057%), neg=0, invalid=766 0251: dt=0.028000, rms=0.422 (0.070%), neg=0, invalid=766 0252: dt=0.028000, rms=0.422 (0.076%), neg=0, invalid=766 0253: dt=0.028000, rms=0.422 (0.017%), neg=0, invalid=766 0254: dt=0.028000, rms=0.422 (0.031%), neg=0, invalid=766 0255: dt=0.028000, rms=0.422 (0.040%), neg=0, invalid=766 0256: dt=0.028000, rms=0.421 (0.053%), neg=0, invalid=766 0257: dt=0.028000, rms=0.421 (0.060%), neg=0, invalid=766 0258: dt=0.028000, rms=0.421 (0.067%), neg=0, invalid=766 0259: dt=0.028000, rms=0.421 (0.075%), neg=0, invalid=766 0260: dt=0.028000, rms=0.420 (0.079%), neg=0, invalid=766 0261: dt=0.028000, rms=0.420 (0.078%), neg=0, invalid=766 0262: dt=0.028000, rms=0.420 (0.085%), neg=0, invalid=766 0263: dt=0.028000, rms=0.419 (0.078%), neg=0, invalid=766 0264: dt=0.028000, rms=0.419 (0.077%), neg=0, invalid=766 0265: dt=0.028000, rms=0.419 (0.076%), neg=0, invalid=766 0266: dt=0.028000, rms=0.418 (0.073%), neg=0, invalid=766 0267: dt=0.028000, rms=0.418 (0.071%), neg=0, invalid=766 0268: dt=0.028000, rms=0.418 (0.066%), neg=0, invalid=766 0269: dt=0.028000, rms=0.418 (0.065%), neg=0, invalid=766 0270: dt=0.028000, rms=0.417 (0.062%), neg=0, invalid=766 0271: dt=0.028000, rms=0.417 (0.057%), neg=0, invalid=766 0272: dt=0.028000, rms=0.417 (0.052%), neg=0, invalid=766 0273: dt=0.028000, rms=0.417 (0.048%), neg=0, invalid=766 0274: dt=0.028000, rms=0.416 (0.045%), neg=0, invalid=766 0275: dt=0.028000, rms=0.416 (0.040%), neg=0, invalid=766 0276: dt=0.028000, rms=0.416 (0.035%), neg=0, invalid=766 0277: dt=0.028000, rms=0.416 (0.044%), neg=0, invalid=766 0278: dt=0.028000, rms=0.416 (0.033%), neg=0, invalid=766 0279: dt=0.028000, rms=0.416 (0.030%), neg=0, invalid=766 0280: dt=0.028000, rms=0.416 (0.029%), neg=0, invalid=766 0281: dt=0.028000, rms=0.415 (0.024%), neg=0, invalid=766 0282: dt=0.028000, rms=0.415 (0.025%), neg=0, invalid=766 0283: dt=0.028000, rms=0.415 (0.018%), neg=0, invalid=766 0284: dt=0.028000, rms=0.415 (0.016%), neg=0, invalid=766 0285: dt=0.448000, rms=0.415 (0.016%), neg=0, invalid=766 0286: dt=0.112000, rms=0.415 (0.002%), neg=0, invalid=766 0287: dt=0.112000, rms=0.415 (0.008%), neg=0, invalid=766 0288: dt=0.112000, rms=0.415 (0.008%), neg=0, invalid=766 0289: dt=0.112000, rms=0.415 (0.010%), neg=0, invalid=766 0290: dt=0.112000, rms=0.415 (0.005%), neg=0, invalid=766 0291: dt=0.112000, rms=0.415 (0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.415, neg=0, invalid=766 0292: dt=0.112000, rms=0.415 (0.070%), neg=0, invalid=766 0293: dt=0.112000, rms=0.414 (0.055%), neg=0, invalid=766 0294: dt=0.112000, rms=0.414 (0.045%), neg=0, invalid=766 0295: dt=0.112000, rms=0.414 (0.027%), neg=0, invalid=766 0296: dt=0.112000, rms=0.414 (0.053%), neg=0, invalid=766 0297: dt=0.112000, rms=0.414 (0.052%), neg=0, invalid=766 0298: dt=0.112000, rms=0.413 (0.054%), neg=0, invalid=766 0299: dt=0.112000, rms=0.413 (0.028%), neg=0, invalid=766 0300: dt=0.112000, rms=0.413 (0.019%), neg=0, invalid=766 0301: dt=0.112000, rms=0.413 (0.004%), neg=0, invalid=766 0302: dt=0.000000, rms=0.413 (0.002%), neg=0, invalid=766 0303: dt=0.050000, rms=0.413 (-0.004%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=766 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0304: dt=44.800000, rms=0.398 (3.209%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 6 iterations, nbhd size=1, neg = 0 0305: dt=44.800000, rms=0.395 (0.875%), neg=0, invalid=766 0306: dt=8.000000, rms=0.394 (0.237%), neg=0, invalid=766 0307: dt=8.000000, rms=0.393 (0.167%), neg=0, invalid=766 0308: dt=8.000000, rms=0.392 (0.173%), neg=0, invalid=766 0309: dt=8.000000, rms=0.392 (0.220%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0310: dt=8.000000, rms=0.391 (0.197%), neg=0, invalid=766 0311: dt=8.000000, rms=0.390 (0.253%), neg=0, invalid=766 0312: dt=8.000000, rms=0.389 (0.232%), neg=0, invalid=766 0313: dt=8.000000, rms=0.388 (0.191%), neg=0, invalid=766 0314: dt=8.000000, rms=0.388 (0.158%), neg=0, invalid=766 0315: dt=8.000000, rms=0.387 (0.156%), neg=0, invalid=766 0316: dt=8.000000, rms=0.386 (0.151%), neg=0, invalid=766 0317: dt=8.000000, rms=0.386 (0.135%), neg=0, invalid=766 0318: dt=8.000000, rms=0.385 (0.109%), neg=0, invalid=766 0319: dt=8.000000, rms=0.385 (0.066%), neg=0, invalid=766 0320: dt=19.200000, rms=0.385 (0.028%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0321: dt=19.200000, rms=0.385 (-0.046%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.385, neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0322: dt=19.200000, rms=0.385 (0.117%), neg=0, invalid=766 0323: dt=9.600000, rms=0.384 (0.098%), neg=0, invalid=766 0324: dt=9.600000, rms=0.384 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0325: dt=9.600000, rms=0.384 (0.055%), neg=0, invalid=766 0326: dt=9.600000, rms=0.383 (0.116%), neg=0, invalid=766 0327: dt=9.600000, rms=0.383 (0.059%), neg=0, invalid=766 0328: dt=9.600000, rms=0.383 (0.060%), neg=0, invalid=766 0329: dt=9.600000, rms=0.383 (0.024%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.388, neg=0, invalid=766 0330: dt=3.456000, rms=0.388 (0.055%), neg=0, invalid=766 0331: dt=1.008000, rms=0.388 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.388, neg=0, invalid=766 0332: dt=2.880000, rms=0.388 (0.024%), neg=0, invalid=766 0333: dt=2.880000, rms=0.388 (0.010%), neg=0, invalid=766 0334: dt=2.880000, rms=0.388 (0.004%), neg=0, invalid=766 0335: dt=2.880000, rms=0.388 (-0.035%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 0336: dt=0.448000, rms=0.395 (0.028%), neg=0, invalid=766 0337: dt=0.448000, rms=0.395 (0.018%), neg=0, invalid=766 0338: dt=0.448000, rms=0.395 (0.001%), neg=0, invalid=766 0339: dt=0.448000, rms=0.395 (-0.046%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.395, neg=0, invalid=766 0340: dt=0.448000, rms=0.395 (0.014%), neg=0, invalid=766 0341: dt=0.448000, rms=0.395 (0.011%), neg=0, invalid=766 0342: dt=0.448000, rms=0.395 (0.001%), neg=0, invalid=766 0343: dt=0.448000, rms=0.395 (-0.028%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 iter 0, gcam->neg = 112 after 9 iterations, nbhd size=1, neg = 0 0344: dt=1.975510, rms=0.367 (4.800%), neg=0, invalid=766 0345: dt=0.005000, rms=0.367 (0.024%), neg=0, invalid=766 0346: dt=0.005000, rms=0.367 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.367, neg=0, invalid=766 0347: dt=0.028000, rms=0.367 (0.010%), neg=0, invalid=766 0348: dt=0.000000, rms=0.367 (0.001%), neg=0, invalid=766 0349: dt=0.050000, rms=0.367 (-0.028%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.357, neg=0, invalid=766 iter 0, gcam->neg = 111 after 17 iterations, nbhd size=2, neg = 0 0350: dt=1.552956, rms=0.347 (2.846%), neg=0, invalid=766 0351: dt=0.000438, rms=0.347 (0.000%), neg=0, invalid=766 0352: dt=0.000438, rms=0.347 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.347, neg=0, invalid=766 0353: dt=0.006000, rms=0.347 (0.001%), neg=0, invalid=766 0354: dt=0.000000, rms=0.347 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.341, neg=0, invalid=766 iter 0, gcam->neg = 139 after 20 iterations, nbhd size=2, neg = 0 0355: dt=1.280000, rms=0.335 (1.954%), neg=0, invalid=766 0356: dt=0.000438, rms=0.335 (-0.036%), neg=0, invalid=766 0357: dt=0.000438, rms=0.335 (0.001%), neg=0, invalid=766 0358: dt=0.000438, rms=0.335 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.335, neg=0, invalid=766 0359: dt=0.000438, rms=0.335 (0.000%), neg=0, invalid=766 0360: dt=0.000008, rms=0.335 (0.000%), neg=0, invalid=766 0361: dt=0.000008, rms=0.335 (-0.000%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.332, neg=0, invalid=766 iter 0, gcam->neg = 10 after 26 iterations, nbhd size=3, neg = 0 0362: dt=25.600000, rms=0.334 (-0.159%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.334, neg=0, invalid=766 iter 0, gcam->neg = 5 after 30 iterations, nbhd size=4, neg = 0 0363: dt=32.000000, rms=0.332 (0.469%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.001 (47.483%) 0364: dt=44.800000, rms=0.331 (0.198%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0365: dt=44.800000, rms=0.331 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 15 iterations, nbhd size=2, neg = 0 0366: dt=44.800000, rms=0.331 (0.156%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 22 iterations, nbhd size=3, neg = 0 0367: dt=44.800000, rms=0.331 (-0.003%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0368: dt=25.600000, rms=0.330 (0.059%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 22 iterations, nbhd size=3, neg = 0 0369: dt=44.800000, rms=0.330 (0.065%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0370: dt=38.400000, rms=0.330 (0.042%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.331, neg=0, invalid=766 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.002, neg=2, removing folds in lattice.... iter 1, dt=0.000188: new neg 0, old_neg 2, delta 2, rms=0.001 (64.236%) 0371: dt=4.032000, rms=0.331 (0.077%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 200 iterations, nbhd size=3, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 1, delta 1, rms=0.000 (58.444%) 0372: dt=9.216000, rms=0.331 (0.085%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 76 iterations, nbhd size=3, neg = 0 0373: dt=9.216000, rms=0.331 (0.075%), neg=0, invalid=766 iter 0, gcam->neg = 14 after 61 iterations, nbhd size=4, neg = 0 0374: dt=9.216000, rms=0.330 (0.049%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 64 iterations, nbhd size=3, neg = 0 0375: dt=9.216000, rms=0.330 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 39 after 65 iterations, nbhd size=3, neg = 0 0376: dt=9.216000, rms=0.330 (0.025%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.330, neg=0, invalid=766 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0377: dt=16.128000, rms=0.329 (0.349%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 15 iterations, nbhd size=2, neg = 0 0378: dt=4.032000, rms=0.329 (0.026%), neg=0, invalid=766 0379: dt=4.032000, rms=0.329 (0.018%), neg=0, invalid=766 0380: dt=4.032000, rms=0.329 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0381: dt=4.032000, rms=0.329 (0.023%), neg=0, invalid=766 0382: dt=4.032000, rms=0.329 (0.025%), neg=0, invalid=766 0383: dt=4.032000, rms=0.329 (0.027%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0384: dt=4.032000, rms=0.328 (0.031%), neg=0, invalid=766 0385: dt=4.032000, rms=0.328 (0.032%), neg=0, invalid=766 0386: dt=4.032000, rms=0.328 (0.031%), neg=0, invalid=766 0387: dt=16.128000, rms=0.328 (0.012%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.331, neg=0, invalid=766 0388: dt=0.000000, rms=0.331 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.331, neg=0, invalid=766 0389: dt=0.000000, rms=0.331 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.327, neg=0, invalid=766 iter 0, gcam->neg = 96 after 31 iterations, nbhd size=1, neg = 0 0390: dt=0.863700, rms=0.323 (1.150%), neg=0, invalid=766 0391: dt=0.000109, rms=0.323 (0.000%), neg=0, invalid=766 0392: dt=0.000109, rms=0.323 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.323, neg=0, invalid=766 0393: dt=0.001750, rms=0.323 (0.000%), neg=0, invalid=766 0394: dt=0.001000, rms=0.323 (0.000%), neg=0, invalid=766 0395: dt=0.001000, rms=0.323 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.322, neg=0, invalid=766 iter 0, gcam->neg = 12 after 7 iterations, nbhd size=1, neg = 0 0396: dt=0.112000, rms=0.321 (0.166%), neg=0, invalid=766 iter 0, gcam->neg = 59 after 22 iterations, nbhd size=3, neg = 0 0397: dt=0.384000, rms=0.320 (0.381%), neg=0, invalid=766 0398: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0399: dt=0.001250, rms=0.320 (0.000%), neg=0, invalid=766 0400: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0401: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0402: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0403: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0404: dt=0.001250, rms=0.320 (0.001%), neg=0, invalid=766 0405: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0406: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0407: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0408: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0409: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0410: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0411: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0412: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0413: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0414: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0415: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0416: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0417: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0418: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 0419: dt=0.001250, rms=0.320 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0420: dt=0.096000, rms=0.320 (0.017%), neg=0, invalid=766 0421: dt=0.004000, rms=0.320 (0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.320, neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0422: dt=0.028000, rms=0.320 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 20 iterations, nbhd size=3, neg = 0 0423: dt=0.028000, rms=0.320 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0424: dt=0.028000, rms=0.320 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0425: dt=0.028000, rms=0.320 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0426: dt=0.028000, rms=0.320 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0427: dt=0.028000, rms=0.319 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0428: dt=0.028000, rms=0.319 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0429: dt=0.028000, rms=0.319 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 7 iterations, nbhd size=1, neg = 0 0430: dt=0.028000, rms=0.319 (0.033%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.319, neg=0, invalid=766 iter 0, gcam->neg = 11 after 20 iterations, nbhd size=3, neg = 0 0431: dt=0.112000, rms=0.318 (0.153%), neg=0, invalid=766 iter 0, gcam->neg = 29 after 8 iterations, nbhd size=1, neg = 0 0432: dt=0.256000, rms=0.317 (0.239%), neg=0, invalid=766 0433: dt=0.001750, rms=0.317 (0.002%), neg=0, invalid=766 0434: dt=0.001750, rms=0.317 (0.001%), neg=0, invalid=766 0435: dt=0.001750, rms=0.317 (0.002%), neg=0, invalid=766 0436: dt=0.001750, rms=0.317 (0.002%), neg=0, invalid=766 0437: dt=0.001750, rms=0.317 (0.003%), neg=0, invalid=766 0438: dt=0.001750, rms=0.317 (0.003%), neg=0, invalid=766 0439: dt=0.001750, rms=0.317 (0.004%), neg=0, invalid=766 0440: dt=0.001750, rms=0.317 (0.004%), neg=0, invalid=766 0441: dt=0.001750, rms=0.317 (0.004%), neg=0, invalid=766 0442: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0443: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0444: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0445: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0446: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0447: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0448: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0449: dt=0.001750, rms=0.317 (0.006%), neg=0, invalid=766 0450: dt=0.001750, rms=0.317 (0.006%), neg=0, invalid=766 0451: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 0452: dt=0.001750, rms=0.317 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.317, neg=0, invalid=766 iter 0, gcam->neg = 6 after 0 iterations, nbhd size=0, neg = 0 0453: dt=0.112000, rms=0.317 (0.072%), neg=0, invalid=766 0454: dt=0.003000, rms=0.317 (0.002%), neg=0, invalid=766 0455: dt=0.003000, rms=0.317 (0.002%), neg=0, invalid=766 0456: dt=0.003000, rms=0.317 (0.003%), neg=0, invalid=766 0457: dt=0.003000, rms=0.317 (0.004%), neg=0, invalid=766 0458: dt=0.003000, rms=0.317 (0.005%), neg=0, invalid=766 0459: dt=0.003000, rms=0.317 (0.006%), neg=0, invalid=766 0460: dt=0.003000, rms=0.317 (0.007%), neg=0, invalid=766 0461: dt=0.003000, rms=0.317 (0.007%), neg=0, invalid=766 0462: dt=0.003000, rms=0.317 (0.008%), neg=0, invalid=766 0463: dt=0.003000, rms=0.317 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0464: dt=0.003000, rms=0.317 (0.008%), neg=0, invalid=766 0465: dt=0.003000, rms=0.317 (0.009%), neg=0, invalid=766 0466: dt=0.003000, rms=0.317 (0.009%), neg=0, invalid=766 0467: dt=0.003000, rms=0.317 (0.009%), neg=0, invalid=766 0468: dt=0.003000, rms=0.317 (0.009%), neg=0, invalid=766 0469: dt=0.003000, rms=0.317 (0.009%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 3 hours, 56 minutes and 51 seconds. #-------------------------------------- #@# CA Reg Inv Fri Mar 30 23:18:07 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Mar 30 23:19:30 EDT 2012 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/dev/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... 10363354 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 12 seconds. #-------------------------------------- #@# SkullLTA Fri Mar 30 23:20:42 EDT 2012 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/dev/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta 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/dev/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=23.0 skull bounding box = (55, 69, 43) --> (196, 197, 213) using (102, 112, 128) as brain centroid... mean wm in atlas = 126, using box (85,96,107) --> (119, 127,148) to find MRI wm before smoothing, mri peak at 112 after smoothing, mri peak at 111, scaling input intensities by 1.135 scaling channel 0 by 1.13514 **************************************** 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) 1.060 -0.018 0.000 -6.326; 0.019 1.176 -0.009 -45.218; -0.000 0.009 1.059 -27.381; 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) 1.139 -0.019 0.000 -16.232; 0.019 1.176 -0.009 -45.218; -0.000 0.009 1.138 -37.387; 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) 1.139 -0.019 0.000 -16.232; 0.019 1.176 -0.009 -45.218; -0.000 0.009 1.138 -37.387; 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=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.117 0.021 0.001 -19.093; -0.017 1.154 0.027 -40.264; -0.001 -0.029 1.117 -31.158; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.138 0.021 0.001 -21.809; -0.017 1.154 0.027 -40.264; -0.001 -0.028 1.096 -28.585; 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=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.138 0.021 0.001 -21.809; -0.017 1.152 0.027 -40.074; -0.001 -0.028 1.098 -28.901; 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 1.13818 0.02098 0.00125 -21.80902; -0.01666 1.15230 0.02717 -40.07421; -0.00074 -0.02803 1.09814 -28.90068; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.13818 0.02098 0.00125 -21.80902; -0.01666 1.15230 0.02717 -40.07421; -0.00074 -0.02803 1.09814 -28.90068; 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: 1.138 0.021 0.001 -21.809; -0.017 1.152 0.027 -40.074; -0.001 -0.028 1.098 -28.901; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.2) transform before final EM align: 1.138 0.021 0.001 -21.809; -0.017 1.152 0.027 -40.074; -0.001 -0.028 1.098 -28.901; 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 1.13818 0.02098 0.00125 -21.80902; -0.01666 1.15230 0.02717 -40.07421; -0.00074 -0.02803 1.09814 -28.90068; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.13818 0.02098 0.00125 -21.80902; -0.01666 1.15230 0.02717 -40.07421; -0.00074 -0.02803 1.09814 -28.90068; 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) = 4.4 tol 0.000000 final transform: 1.138 0.021 0.001 -21.809; -0.017 1.152 0.027 -40.074; -0.001 -0.028 1.098 -28.901; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 24 minutes and 45 seconds. #-------------------------------------- #@# SubCort Seg Fri Mar 30 23:45:28 EDT 2012 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname compute-0-104.local machine x86_64 setenv SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/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 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /usr/local/freesurfer/dev/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/dev/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 = 0.08937 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (2354 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2354 voxels, peak = 3), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.13460 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.10 x + 0.0 (1872 voxels, overlap=0.000) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1872 voxels, peak = 2), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.16302 (91) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (503 voxels, overlap=0.000) Right_Pallidum (52): linear fit = 0.93 x + 0.0 (503 voxels, peak = 90), gca=89.7 gca peak = 0.18160 (96) mri peak = 0.16330 (91) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (545 voxels, overlap=0.180) Left_Pallidum (13): linear fit = 0.93 x + 0.0 (545 voxels, peak = 89), gca=88.8 gca peak = 0.27536 (62) mri peak = 0.19355 (50) Right_Hippocampus (53): linear fit = 0.77 x + 0.0 (1732 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 0.77 x + 0.0 (1732 voxels, peak = 48), gca=48.0 gca peak = 0.32745 (63) mri peak = 0.13353 (54) Left_Hippocampus (17): linear fit = 0.77 x + 0.0 (1683 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 0.77 x + 0.0 (1683 voxels, peak = 49), gca=48.8 gca peak = 0.08597 (105) mri peak = 0.10390 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (69787 voxels, overlap=0.653) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (69787 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.10481 (105) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (80481 voxels, overlap=0.661) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (80481 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.05645 (54) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (83753 voxels, overlap=0.445) Left_Cerebral_Cortex (3): linear fit = 0.82 x + 0.0 (83753 voxels, peak = 52), gca=52.0 gca peak = 0.08598 (64) mri peak = 0.05842 (51) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (86316 voxels, overlap=0.347) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (86316 voxels, peak = 53), gca=52.8 gca peak = 0.24164 (71) mri peak = 0.09369 (61) Right_Caudate (50): linear fit = 0.85 x + 0.0 (1311 voxels, overlap=0.000) Right_Caudate (50): linear fit = 0.85 x + 0.0 (1311 voxels, peak = 60), gca=60.4 gca peak = 0.18227 (75) mri peak = 0.07988 (65) Left_Caudate (11): linear fit = 0.82 x + 0.0 (1346 voxels, overlap=0.000) Left_Caudate (11): linear fit = 0.82 x + 0.0 (1346 voxels, peak = 62), gca=61.9 gca peak = 0.10629 (62) mri peak = 0.07959 (62) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (40029 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (40029 voxels, peak = 62), gca=62.0 gca peak = 0.11668 (59) mri peak = 0.07841 (62) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42942 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42942 voxels, peak = 59), gca=59.0 gca peak = 0.17849 (88) mri peak = 0.14595 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9611 voxels, overlap=0.920) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (9611 voxels, peak = 90), gca=90.2 gca peak = 0.16819 (86) mri peak = 0.15402 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8752 voxels, overlap=0.895) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8752 voxels, peak = 88), gca=88.2 gca peak = 0.41688 (64) mri peak = 0.20333 (54) Left_Amygdala (18): linear fit = 0.82 x + 0.0 (595 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 0.82 x + 0.0 (595 voxels, peak = 53), gca=52.8 gca peak = 0.42394 (62) mri peak = 0.16651 (54) Right_Amygdala (54): linear fit = 0.82 x + 0.0 (681 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 0.82 x + 0.0 (681 voxels, peak = 51), gca=51.1 gca peak = 0.10041 (96) mri peak = 0.10599 (84) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (6149 voxels, overlap=0.288) Left_Thalamus_Proper (10): linear fit = 0.88 x + 0.0 (6149 voxels, peak = 84), gca=84.0 gca peak = 0.13978 (88) mri peak = 0.10005 (83) Right_Thalamus_Proper (49): linear fit = 0.90 x + 0.0 (6145 voxels, overlap=0.484) Right_Thalamus_Proper (49): linear fit = 0.90 x + 0.0 (6145 voxels, peak = 79), gca=79.2 gca peak = 0.08514 (81) mri peak = 0.07037 (69) Left_Putamen (12): linear fit = 0.85 x + 0.0 (2972 voxels, overlap=0.370) Left_Putamen (12): linear fit = 0.85 x + 0.0 (2972 voxels, peak = 69), gca=68.8 gca peak = 0.09624 (82) mri peak = 0.08038 (67) Right_Putamen (51): linear fit = 0.85 x + 0.0 (2849 voxels, overlap=0.313) Right_Putamen (51): linear fit = 0.85 x + 0.0 (2849 voxels, peak = 70), gca=69.7 gca peak = 0.07543 (88) mri peak = 0.09836 (86) Brain_Stem (16): linear fit = 0.98 x + 0.0 (17997 voxels, overlap=0.698) Brain_Stem (16): linear fit = 0.98 x + 0.0 (17997 voxels, peak = 86), gca=85.8 gca peak = 0.12757 (95) mri peak = 0.08595 (96) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (2013 voxels, overlap=0.837) Right_VentralDC (60): linear fit = 0.98 x + 0.0 (2013 voxels, peak = 93), gca=92.6 gca peak = 0.17004 (92) mri peak = 0.08742 (96) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2173 voxels, overlap=0.840) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2173 voxels, peak = 90), gca=89.7 gca peak = 0.21361 (36) mri peak = 0.06788 (46) gca peak = 0.26069 (23) mri peak = 0.11751 ( 2) Fourth_Ventricle (15): linear fit = 0.03 x + 0.0 (360 voxels, overlap=0.000) Fourth_Ventricle (15): linear fit = 0.03 x + 0.0 (360 voxels, peak = 1), gca=0.6 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 0.81 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 = 0.08937 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.35 x + 0.0 (2354 voxels, overlap=0.967) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (2354 voxels, peak = 4), gca=4.4 gca peak = 0.29325 ( 9) mri peak = 0.13460 ( 3) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (1872 voxels, overlap=0.965) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (1872 voxels, peak = 2), gca=3.6 gca peak = 0.30146 (90) mri peak = 0.16302 (91) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (503 voxels, overlap=0.998) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (503 voxels, peak = 88), gca=87.8 gca peak = 0.18434 (89) mri peak = 0.16330 (91) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (545 voxels, overlap=1.000) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (545 voxels, peak = 87), gca=86.8 gca peak = 0.35598 (48) mri peak = 0.19355 (50) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1732 voxels, overlap=0.998) Right_Hippocampus (53): linear fit = 1.02 x + 0.0 (1732 voxels, peak = 49), gca=49.2 gca peak = 0.39946 (49) mri peak = 0.13353 (54) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1683 voxels, overlap=0.996) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1683 voxels, peak = 50), gca=50.2 gca peak = 0.08348 (108) mri peak = 0.10390 (105) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (69787 voxels, overlap=0.715) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (69787 voxels, peak = 108), gca=108.0 gca peak = 0.08790 (111) mri peak = 0.10481 (105) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (80481 voxels, overlap=0.756) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (80481 voxels, peak = 108), gca=108.2 gca peak = 0.09550 (52) mri peak = 0.05645 (54) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (83753 voxels, overlap=0.997) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (83753 voxels, peak = 53), gca=53.3 gca peak = 0.10540 (53) mri peak = 0.05842 (51) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (86316 voxels, overlap=0.992) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (86316 voxels, peak = 52), gca=51.7 gca peak = 0.24090 (60) mri peak = 0.09369 (61) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1311 voxels, overlap=0.995) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1311 voxels, peak = 60), gca=60.0 gca peak = 0.16665 (62) mri peak = 0.07988 (65) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1346 voxels, overlap=0.990) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1346 voxels, peak = 62), gca=62.0 gca peak = 0.10561 (62) mri peak = 0.07959 (62) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (40029 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (40029 voxels, peak = 62), gca=62.0 gca peak = 0.11735 (59) mri peak = 0.07841 (62) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42942 voxels, overlap=0.988) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42942 voxels, peak = 59), gca=59.0 gca peak = 0.16635 (89) mri peak = 0.14595 (90) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (9611 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (9611 voxels, peak = 89), gca=89.0 gca peak = 0.14595 (89) mri peak = 0.15402 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8752 voxels, overlap=0.965) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (8752 voxels, peak = 89), gca=89.0 gca peak = 0.41074 (52) mri peak = 0.20333 (54) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (595 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (595 voxels, peak = 52), gca=52.0 gca peak = 0.47565 (52) mri peak = 0.16651 (54) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (681 voxels, overlap=0.997) Right_Amygdala (54): linear fit = 1.02 x + 0.0 (681 voxels, peak = 53), gca=53.3 gca peak = 0.10688 (84) mri peak = 0.10599 (84) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6149 voxels, overlap=0.966) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6149 voxels, peak = 84), gca=84.0 gca peak = 0.13261 (79) mri peak = 0.10005 (83) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6145 voxels, overlap=0.908) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (6145 voxels, peak = 79), gca=79.0 gca peak = 0.11225 (70) mri peak = 0.07037 (69) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2972 voxels, overlap=0.965) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2972 voxels, peak = 70), gca=70.0 gca peak = 0.10658 (70) mri peak = 0.08038 (67) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2849 voxels, overlap=1.000) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2849 voxels, peak = 70), gca=70.0 gca peak = 0.07943 (86) mri peak = 0.09836 (86) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17997 voxels, overlap=0.686) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17997 voxels, peak = 86), gca=86.0 gca peak = 0.13913 (92) mri peak = 0.08595 (96) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2013 voxels, overlap=0.805) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2013 voxels, peak = 92), gca=92.0 gca peak = 0.14642 (90) mri peak = 0.08742 (96) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2173 voxels, overlap=0.897) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (2173 voxels, peak = 90), gca=90.0 gca peak = 0.35640 (14) mri peak = 0.06788 (46) gca peak = 0.33827 ( 9) mri peak = 0.11751 ( 2) Fourth_Ventricle (15): linear fit = 0.10 x + 0.0 (360 voxels, overlap=0.109) Fourth_Ventricle (15): linear fit = 0.10 x + 0.0 (360 voxels, peak = 1), gca=0.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.33163 (27) gca peak Third_Ventricle = 0.35640 (14) gca peak Fourth_Ventricle = 0.33827 ( 9) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.51409 (58) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.44155 (61) gca peak Left_choroid_plexus = 0.09166 (48) gca peak Right_Inf_Lat_Vent = 0.33209 (25) gca peak Right_Accumbens_area = 0.46484 (61) gca peak Right_vessel = 0.57697 (60) gca peak Right_choroid_plexus = 0.13071 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.14020 (85) gca peak non_WM_hypointensities = 0.10106 (55) gca peak Optic_Chiasm = 0.34849 (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 0.99 x + 0.0 estimating mean csf scale to be 0.40 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 16662 gm and wm labels changed (%21 to gray, %79 to white out of all changed labels) 453 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 96907 changed. image ll: -2.203, PF=1.000 pass 2: 16012 changed. image ll: -2.201, PF=1.000 pass 3: 7699 changed. pass 4: 4293 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 20 minutes and 32 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/transforms/cc_up.lta cvs_avg35_inMNI152 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/transforms/cc_up.lta reading aseg from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/norm.mgz 28256 voxels in left wm, 21974 in right wm, xrange [124, 131] searching rotation angles z=[-7 7], y=[-8 6] searching scale 1 Z rot -7.2 searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 global minimum found at slice 126.2, rotations (-0.50, -0.23) final transformation (x=126.2, yr=-0.503, zr=-0.230): 1.000 0.004 -0.009 2.256; -0.004 1.000 0.000 0.504; 0.009 0.000 1.000 16.897; 0.000 0.000 0.000 1.000; updating x range to be [126, 132] in xformed coordinates best xformed slice 128 cc center is found at 128 149 183 eigenvectors: -0.000 -0.002 1.000; 0.149 -0.989 -0.002; 0.989 0.149 0.000; error in mid anterior detected - correcting... writing aseg with callosum to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.7 minutes #-------------------------------------- #@# Merge ASeg Sat Mar 31 00:06:43 EDT 2012 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Mar 31 00:06:44 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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... 5573 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 109 gm peak at 55 (55), valley at 0 (-1) csf peak at 27, setting threshold to 45 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 58 (58), valley at 31 (31) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 42 seconds. #-------------------------------------------- #@# Mask BFS Sat Mar 31 00:10:29 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1956156 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Mar 31 00:10:31 EDT 2012 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 (103.0): 103.3 +- 4.6 [80.0 --> 119.0] GM (74.0) : 74.0 +- 7.7 [30.0 --> 96.0] setting bottom of white matter range to 81.8 setting top of gray matter range to 89.5 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... 489 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1598 filled 0 bright non-wm voxels segmented. 529 diagonally connected voxels added... white matter segmentation took 1.8 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 0.73 minutes reading wm segmentation from wm.seg.mgz... 360 voxels added to wm to prevent paths from MTL structures to cortex 2252 additional wm voxels added 0 additional wm voxels added SEG EDIT: 56261 voxels turned on, 66045 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 10 found - 10 modified | TOTAL: 15 pass 2 (xy-): 0 found - 10 modified | TOTAL: 15 pass 1 (yz+): 14 found - 14 modified | TOTAL: 29 pass 2 (yz+): 0 found - 14 modified | TOTAL: 29 pass 1 (yz-): 11 found - 11 modified | TOTAL: 40 pass 2 (yz-): 0 found - 11 modified | TOTAL: 40 pass 1 (xz+): 20 found - 20 modified | TOTAL: 60 pass 2 (xz+): 0 found - 20 modified | TOTAL: 60 pass 1 (xz-): 10 found - 10 modified | TOTAL: 70 pass 2 (xz-): 0 found - 10 modified | TOTAL: 70 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 3 found - 3 modified | TOTAL: 15 pass 2 (+++): 0 found - 3 modified | TOTAL: 15 pass 1 (+++): 0 found - 0 modified | TOTAL: 15 Iteration Number : 1 pass 1 (++): 22 found - 22 modified | TOTAL: 22 pass 2 (++): 0 found - 22 modified | TOTAL: 22 pass 1 (+-): 37 found - 37 modified | TOTAL: 59 pass 2 (+-): 0 found - 37 modified | TOTAL: 59 pass 1 (--): 29 found - 29 modified | TOTAL: 88 pass 2 (--): 1 found - 30 modified | TOTAL: 89 pass 3 (--): 0 found - 30 modified | TOTAL: 89 pass 1 (-+): 16 found - 16 modified | TOTAL: 105 pass 2 (-+): 0 found - 16 modified | TOTAL: 105 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 1 found - 1 modified | TOTAL: 4 pass 2 (yz-): 0 found - 1 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 1 found - 1 modified | TOTAL: 5 pass 2 (xz-): 0 found - 1 modified | TOTAL: 5 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 6 found - 6 modified | TOTAL: 6 pass 2 (+++): 0 found - 6 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 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 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 205 (out of 725492: 0.028257) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Mar 31 00:13:10 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.996 -0.017 0.000 1.590; 0.016 1.023 -0.008 -23.523; -0.000 0.008 0.995 -19.385; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2829 (min = 350, max = 1400), aspect = 1.26 (min = 0.10, max = 0.75) need search nearby using seed (124, 116, 89), TAL = (4.0, -39.0, 12.0) talairach voxel to voxel transform 1.003 0.016 -0.000 -1.215; -0.016 0.978 0.008 23.177; 0.000 -0.008 1.005 19.285; 0.000 0.000 0.000 1.000; segmentation indicates cc at (124, 116, 89) --> (4.0, -39.0, 12.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (4.00, -39.00, 12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(22.00, -39.00, 12.00) SRC: (107.02, 135.58, 107.79) search lh wm seed point around talairach space (-14.00, -39.00, 12.00), SRC: (143.14, 135.00, 107.80) 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 Sat Mar 31 00:14:05 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 6 found - 6 modified | TOTAL: 12 pass 2 (xz+): 0 found - 6 modified | TOTAL: 12 pass 1 (xz-): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 1 found - 1 modified | TOTAL: 3 pass 2 (-+): 0 found - 1 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 15 (out of 352126: 0.004260) 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 1.721 2012/03/08 13:49:42 fischl Exp $ slice 50: 2412 vertices, 2544 faces slice 60: 7778 vertices, 8025 faces slice 70: 14768 vertices, 15047 faces slice 80: 23317 vertices, 23610 faces slice 90: 33248 vertices, 33610 faces slice 100: 42772 vertices, 43064 faces slice 110: 53950 vertices, 54335 faces slice 120: 66529 vertices, 66918 faces slice 130: 78061 vertices, 78470 faces slice 140: 89786 vertices, 90145 faces slice 150: 100433 vertices, 100872 faces slice 160: 109271 vertices, 109563 faces slice 170: 116517 vertices, 116781 faces slice 180: 123831 vertices, 124101 faces slice 190: 129778 vertices, 129989 faces slice 200: 134521 vertices, 134710 faces slice 210: 138143 vertices, 138229 faces slice 220: 138780 vertices, 138800 faces slice 230: 138780 vertices, 138800 faces slice 240: 138780 vertices, 138800 faces slice 250: 138780 vertices, 138800 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... 138780 voxel in cpt #1: X=-20 [v=138780,e=416400,f=277600] located at (-28.482050, -5.125299, -1.687714) For the whole surface: X=-20 [v=138780,e=416400,f=277600] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Mar 31 00:14:14 EDT 2012 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 00:14:20 EDT 2012 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 49.9 mm, total surface area = 77776 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.087 (target=0.015) step 005: RMS=0.065 (target=0.015) step 010: RMS=0.050 (target=0.015) step 015: RMS=0.041 (target=0.015) step 020: RMS=0.036 (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=0.023 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Sat Mar 31 00:15:09 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... scaling brain by 0.309... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.724, avgs=0 005/300: dt: 0.9000, rms radial error=176.464, avgs=0 010/300: dt: 0.9000, rms radial error=175.906, avgs=0 015/300: dt: 0.9000, rms radial error=175.173, avgs=0 020/300: dt: 0.9000, rms radial error=174.338, avgs=0 025/300: dt: 0.9000, rms radial error=173.444, avgs=0 030/300: dt: 0.9000, rms radial error=172.518, avgs=0 035/300: dt: 0.9000, rms radial error=171.577, avgs=0 040/300: dt: 0.9000, rms radial error=170.633, avgs=0 045/300: dt: 0.9000, rms radial error=169.688, avgs=0 050/300: dt: 0.9000, rms radial error=168.743, avgs=0 055/300: dt: 0.9000, rms radial error=167.801, avgs=0 060/300: dt: 0.9000, rms radial error=166.863, avgs=0 065/300: dt: 0.9000, rms radial error=165.929, avgs=0 070/300: dt: 0.9000, rms radial error=165.000, avgs=0 075/300: dt: 0.9000, rms radial error=164.076, avgs=0 080/300: dt: 0.9000, rms radial error=163.157, avgs=0 085/300: dt: 0.9000, rms radial error=162.242, avgs=0 090/300: dt: 0.9000, rms radial error=161.333, avgs=0 095/300: dt: 0.9000, rms radial error=160.428, avgs=0 100/300: dt: 0.9000, rms radial error=159.528, avgs=0 105/300: dt: 0.9000, rms radial error=158.633, avgs=0 110/300: dt: 0.9000, rms radial error=157.743, avgs=0 115/300: dt: 0.9000, rms radial error=156.858, avgs=0 120/300: dt: 0.9000, rms radial error=155.977, avgs=0 125/300: dt: 0.9000, rms radial error=155.101, avgs=0 130/300: dt: 0.9000, rms radial error=154.230, avgs=0 135/300: dt: 0.9000, rms radial error=153.364, avgs=0 140/300: dt: 0.9000, rms radial error=152.502, avgs=0 145/300: dt: 0.9000, rms radial error=151.645, avgs=0 150/300: dt: 0.9000, rms radial error=150.792, avgs=0 155/300: dt: 0.9000, rms radial error=149.945, avgs=0 160/300: dt: 0.9000, rms radial error=149.101, avgs=0 165/300: dt: 0.9000, rms radial error=148.263, avgs=0 170/300: dt: 0.9000, rms radial error=147.429, avgs=0 175/300: dt: 0.9000, rms radial error=146.601, avgs=0 180/300: dt: 0.9000, rms radial error=145.777, avgs=0 185/300: dt: 0.9000, rms radial error=144.958, avgs=0 190/300: dt: 0.9000, rms radial error=144.144, avgs=0 195/300: dt: 0.9000, rms radial error=143.333, avgs=0 200/300: dt: 0.9000, rms radial error=142.528, avgs=0 205/300: dt: 0.9000, rms radial error=141.726, avgs=0 210/300: dt: 0.9000, rms radial error=140.929, avgs=0 215/300: dt: 0.9000, rms radial error=140.136, avgs=0 220/300: dt: 0.9000, rms radial error=139.348, avgs=0 225/300: dt: 0.9000, rms radial error=138.564, avgs=0 230/300: dt: 0.9000, rms radial error=137.784, avgs=0 235/300: dt: 0.9000, rms radial error=137.009, avgs=0 240/300: dt: 0.9000, rms radial error=136.238, avgs=0 245/300: dt: 0.9000, rms radial error=135.471, avgs=0 250/300: dt: 0.9000, rms radial error=134.709, avgs=0 255/300: dt: 0.9000, rms radial error=133.951, avgs=0 260/300: dt: 0.9000, rms radial error=133.197, avgs=0 265/300: dt: 0.9000, rms radial error=132.447, avgs=0 270/300: dt: 0.9000, rms radial error=131.701, avgs=0 275/300: dt: 0.9000, rms radial error=130surface projected - minimizing metric distortion... vertex spacing 0.99 +- 0.55 (0.00-->5.70) (max @ vno 43426 --> 44349) face area 0.03 +- 0.03 (-0.07-->0.54) .960, avgs=0 280/300: dt: 0.9000, rms radial error=130.223, avgs=0 285/300: dt: 0.9000, rms radial error=129.490, avgs=0 290/300: dt: 0.9000, rms radial error=128.761, avgs=0 295/300: dt: 0.9000, rms radial error=128.036, avgs=0 300/300: dt: 0.9000, rms radial error=127.315, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 16084.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 2606.25 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 3 (K=160.0), pass 1, starting sse = 240.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/12 = 0.00892 epoch 4 (K=640.0), pass 1, starting sse = 11.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/14 = 0.00786 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sat Mar 31 00:21:13 EDT 2012 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 cvs_avg35_inMNI152 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 1.721 2012/03/08 13:49:42 fischl Exp $ before topology correction, eno=-20 (nv=138780, nf=277600, ne=416400, 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... 2681 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 15 defects to be corrected 0 vertices coincident reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9302 (-4.4651) -vertex loglikelihood: -5.9542 (-2.9771) -normal dot loglikelihood: -3.6359 (-3.6359) -quad curv loglikelihood: -6.2114 (-3.1057) Total Loglikelihood : -24.7316 CORRECTING DEFECT 0 (vertices=205, convex hull=76) After retessellation of defect 0, euler #=-12 (137289,411546,274245) : difference with theory (-12) = 0 CORRECTING DEFECT 1 (vertices=5, convex hull=19) After retessellation of defect 1, euler #=-11 (137289,411549,274249) : difference with theory (-11) = 0 CORRECTING DEFECT 2 (vertices=56, convex hull=73) After retessellation of defect 2, euler #=-10 (137316,411661,274335) : difference with theory (-10) = 0 CORRECTING DEFECT 3 (vertices=15, convex hull=33) After retessellation of defect 3, euler #=-9 (137321,411687,274357) : difference with theory (-9) = 0 CORRECTING DEFECT 4 (vertices=33, convex hull=15) After retessellation of defect 4, euler #=-8 (137324,411699,274367) : difference with theory (-8) = 0 CORRECTING DEFECT 5 (vertices=177, convex hull=140) After retessellation of defect 5, euler #=-7 (137347,411831,274477) : difference with theory (-7) = 0 CORRECTING DEFECT 6 (vertices=18, convex hull=68) After retessellation of defect 6, euler #=-6 (137356,411884,274522) : difference with theory (-6) = 0 CORRECTING DEFECT 7 (vertices=33, convex hull=75) After retessellation of defect 7, euler #=-5 (137364,411938,274569) : difference with theory (-5) = 0 CORRECTING DEFECT 8 (vertices=43, convex hull=46) After retessellation of defect 8, euler #=-4 (137373,411982,274605) : difference with theory (-4) = 0 CORRECTING DEFECT 9 (vertices=22, convex hull=43) After retessellation of defect 9, euler #=-3 (137382,412028,274643) : difference with theory (-3) = 0 CORRECTING DEFECT 10 (vertices=786, convex hull=98) After retessellation of defect 10, euler #=-2 (137391,412099,274706) : difference with theory (-2) = 0 CORRECTING DEFECT 11 (vertices=36, convex hull=44) After retessellation of defect 11, euler #=-1 (137400,412140,274739) : difference with theory (-1) = 0 CORRECTING DEFECT 12 (vertices=34, convex hull=56) After retessellation of defect 12, euler #=0 (137411,412196,274785) : difference with theory (0) = 0 CORRECTING DEFECT 13 (vertices=21, convex hull=34) After retessellation of defect 13, euler #=1 (137418,412228,274811) : difference with theory (1) = 0 CORRECTING DEFECT 14 (vertices=24, convex hull=52) After retessellation of defect 14, euler #=2 (137427,412275,274850) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.09-->11.43) (max @ vno 51990 --> 56537) 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 (0.09-->11.43) (max @ vno 51990 --> 56537) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 78 mutations (33.6%), 154 crossovers (66.4%), 154 vertices were eliminated building final representation... 1353 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137427, nf=274850, ne=412275, g=0) writing corrected surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 15.6 minutes 0 defective edges removing intersecting faces 000: 96 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 137427 - 412275 + 274850 = 2 --> 0 holes F =2V-4: 274850 = 274854-4 (0) 2E=3F: 824550 = 824550 (0) total defect index = 0 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 18 intersecting 001: 23 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Mar 31 00:36:57 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs cvs_avg35_inMNI152 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 1.130 2011/12/08 15:01:24 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/filled.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/brain.finalsurfs.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... 5105 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.orig... computing class statistics... border white: 261470 voxels (1.56%) border gray 278696 voxels (1.66%) WM (94.0): 94.6 +- 7.0 [70.0 --> 110.0] GM (83.0) : 80.3 +- 11.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.6 (was 70) setting MAX_BORDER_WHITE to 108.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 46.2 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.84 +- 0.21 (0.03-->4.34) (max @ vno 51990 --> 56537) face area 0.29 +- 0.12 (0.00-->2.43) mean absolute distance = 0.93 +- 1.24 5383 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=69 using class modes intead of means.... mean inside = 92.2, mean outside = 76.5 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.5, 145 (145) missing vertices, mean dist -0.1 [1.2 (%39.8)->0.7 (%60.2))] %67 local maxima, %24 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.89 +- 0.23 (0.05-->4.37) (max @ vno 54244 --> 54245) face area 0.29 +- 0.13 (0.00-->2.61) 000: dt: 0.0000, sse=3443661.0, rms=7.81 001: dt: 0.5000, sse=4384173.0, rms=5.17 002: dt: 0.5000, sse=4771672.5, rms=3.77 003: dt: 0.5000, sse=5146705.5, rms=3.14 004: dt: 0.5000, sse=5312636.0, rms=2.90 005: dt: 0.5000, sse=5442876.0, rms=2.83 rms = 2.82, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=5452960.0, rms=2.82 007: dt: 0.2500, sse=2910110.0, rms=1.74 008: dt: 0.2500, sse=2627171.5, rms=1.52 rms = 1.47, time step reduction 2 of 3 to 0.125... 009: dt: 0.2500, sse=2502461.5, rms=1.47 rms = 1.43, time step reduction 3 of 3 to 0.062... 010: dt: 0.1250, sse=2448657.2, rms=1.43 positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped mean absolute distance = 0.61 +- 1.10 5951 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.2, 108 (40) missing vertices, mean dist -0.3 [0.8 (%59.6)->0.4 (%40.4))] %77 local maxima, %15 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 = 0.500 vertex spacing 0.88 +- 0.23 (0.06-->4.61) (max @ vno 54244 --> 54245) face area 0.33 +- 0.15 (0.00-->3.40) 000: dt: 0.0000, sse=2872655.2, rms=4.12 011: dt: 0.5000, sse=3200222.5, rms=2.56 012: dt: 0.5000, sse=3727905.8, rms=2.36 rms = 2.33, time step reduction 1 of 3 to 0.250... 013: dt: 0.5000, sse=3978418.0, rms=2.33 014: dt: 0.2500, sse=2810577.5, rms=1.36 015: dt: 0.2500, sse=2642754.5, rms=1.14 rms = 1.10, time step reduction 2 of 3 to 0.125... 016: dt: 0.2500, sse=2554126.8, rms=1.10 rms = 1.07, time step reduction 3 of 3 to 0.062... 017: dt: 0.1250, sse=2517747.0, rms=1.07 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.0, 112 (28) missing vertices, mean dist -0.2 [0.6 (%52.7)->0.3 (%47.3))] %83 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignmean absolute distance = 0.48 +- 0.84 5017 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... ored tol=1.0e-04, sigma=0.5, host=compu, 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 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 = 0.250 vertex spacing 0.88 +- 0.23 (0.10-->4.59) (max @ vno 54244 --> 54245) face area 0.32 +- 0.14 (0.00-->3.58) 000: dt: 0.0000, sse=2637097.0, rms=2.50 018: dt: 0.5000, sse=2918972.0, rms=1.82 rms = 1.96, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=2710133.2, rms=1.36 020: dt: 0.2500, sse=2673646.8, rms=1.11 021: dt: 0.2500, sse=2639263.8, rms=1.05 rms = 1.04, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=2622788.0, rms=1.04 rms = 1.02, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=2599908.2, rms=1.02 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=85.2, 80 (19) missing vertices, mean dist -0.1 [0.6 (%47.7)->0.3 (%52.3))] %85 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignmean absolute distance = 0.44 +- 0.73 4596 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... ored tol=1.0e-04, sigma=0.2, host=compu, 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 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 writing white matter surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... 000: dt: 0.0000, sse=2661851.5, rms=1.90 024: dt: 0.5000, sse=3325797.0, rms=1.33 rms = 1.64, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3038911.2, rms=1.01 026: dt: 0.2500, sse=2930884.2, rms=0.90 rms = 0.86, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=2963295.5, rms=0.86 rms = 0.85, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=2957794.5, rms=0.85 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 17 non-cortical segments detected only using segment with 1926 vertices erasing segment 1 (vno[0] = 71975) erasing segment 2 (vno[0] = 74171) erasing segment 3 (vno[0] = 76298) erasing segment 4 (vno[0] = 78288) erasing segment 5 (vno[0] = 78635) erasing segment 6 (vno[0] = 79902) erasing segment 7 (vno[0] = 82132) erasing segment 8 (vno[0] = 87772) erasing segment 9 (vno[0] = 88875) erasing segment 10 (vno[0] = 90815) erasing segment 11 (vno[0] = 92732) erasing segment 12 (vno[0] = 99052) erasing segmewriting smoothed curvature to lh.curv nt 13 (vno[0] = 105205) erasing segment 14 (vno[0] = 105963) erasing segment 15 (vno[0] = 106759) erasing segment 16 (vno[0] = 106777) writing cortex label to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label... LabelWrite: saving to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.area vertex spacing 0.88 +- 0.23 (0.06-->4.60) (max @ vno 54244 --> 54245) face area 0.32 +- 0.14 (0.00-->3.83) refinement took 4.9 minutes #-------------------------------------------- #@# Smooth2 lh Sat Mar 31 00:41:55 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 00:42:00 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 50.0 mm, total surface area = 83128 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.098 (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=0.035 (target=0.015) step 025: RMS=0.029 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.8 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 285 vertices thresholded to be in k1 ~ [-0.24 0.33], k2 ~ [-0.09 0.05] total integrated curvature = 0.502*4pi (6.307) --> 0 handles ICI = 1.8, FI = 12.8, variation=214.971 157 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 139 vertices thresholded to be in [-0.14 0.17] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.028 done. #----------------------------------------- #@# Curvature Stats lh Sat Mar 31 00:44:23 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm cvs_avg35_inMNI152 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 [ cvs_avg35_inMNI152/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: -1.148597 WARN: S explicit min: 0.000000 vertex = 20 #-------------------------------------------- #@# Sphere lh Sat Mar 31 00:44:31 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.299... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=compu, 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 %19.24 pass 1: epoch 2 of 3 starting distance error %19.20 unfolding complete - removing small folds... starting distance error %19.17 removing remaining folds... final distance error %19.19 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.83 hours #-------------------------------------------- #@# Surf Reg lh Sat Mar 31 01:34:08 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.60 2011/09/20 17:53:32 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/dev/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=compu, 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=compu, 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 -------------------- 1 Reading lh.sulc curvature mean = 0.000, std = 0.619 curvature mean = 0.039, std = 0.931 curvature mean = 0.011, std = 0.880 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 314664.8, tmin=1.2676 d=32.00 min @ (0.00, 8.00, 0.00) sse = 190006.1, tmin=2.5463 d=8.00 min @ (2.00, 0.00, -2.00) sse = 177663.9, tmin=5.1184 d=4.00 min @ (0.00, 1.00, 0.00) sse = 175643.4, tmin=6.4156 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 175553.3, tmin=9.0151 d=0.50 min @ (0.12, 0.00, 0.00) sse = 175523.6, tmin=10.3267 tol=1.0e+00, sigma=0.5, host=compu, 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 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 MRISrigidBodyAlignGlobal() done 10.33 min curvature mean = 0.017, std = 0.958 curvature mean = 0.004, std = 0.956 curvature mean = 0.016, std = 0.972 curvature mean = 0.002, std = 0.982 curvature mean = 0.016, std = 0.976 curvature mean = 0.001, std = 0.993 2 Reading smoothwm curvature mean = -0.025, std = 0.238 curvature mean = 0.004, std = 0.068 curvature mean = 0.035, std = 0.396 curvature mean = 0.003, std = 0.081 curvature mean = 0.019, std = 0.575 curvature mean = 0.003, std = 0.088 curvature mean = 0.009, std = 0.702 curvature mean = 0.003, std = 0.092 curvature mean = 0.003, std = 0.796 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat Mar 31 02:41:52 EDT 2012 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 Sat Mar 31 02:41:55 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/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/dev/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat Mar 31 02:41:57 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 cvs_avg35_inMNI152 lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 1352 labels changed using aseg relabeling using gibbs priors... 000: 3017 changed, 137427 examined... 001: 656 changed, 12858 examined... 002: 151 changed, 3766 examined... 003: 46 changed, 928 examined... 004: 15 changed, 273 examined... 005: 10 changed, 96 examined... 006: 7 changed, 55 examined... 007: 6 changed, 36 examined... 008: 7 changed, 30 examined... 009: 1 changed, 37 examined... 010: 1 changed, 7 examined... 011: 2 changed, 7 examined... 012: 3 changed, 10 examined... 013: 1 changed, 13 examined... 014: 0 changed, 7 examined... 235 labels changed using aseg 000: 138 total segments, 95 labels (278 vertices) changed 001: 44 total segments, 1 labels (3 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1454 vertices marked for relabeling... 1454 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 52 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Mar 31 02:42:50 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs cvs_avg35_inMNI152 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 1.130 2011/12/08 15:01:24 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/filled.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/brain.finalsurfs.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... 5105 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.orig... computing class statistics... border white: 261470 voxels (1.56%) border gray 278696 voxels (1.66%) WM (94.0): 94.6 +- 7.0 [70.0 --> 110.0] GM (83.0) : 80.3 +- 11.4 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.6 (was 70) setting MAX_BORDER_WHITE to 108.0 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 46.2 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.8 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=69 using class modes intead of means.... mean inside = 92.2, mean outside = 76.5 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.84 +- 0.21 (0.03-->4.34) (max @ vno 51990 --> 56537) face area 0.29 +- 0.12 (0.00-->2.43) inhibiting deformation at non-cortical midline structures... deleting segment 0 with 204 points - only 10.78% unknown deleting segment 2 with 6 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 16 points - only 0.00% unknown deleting segment 6 with 710 points - only 0.00% unknown deleting segment 7 with 37 points - only 0.00% unknown deleting segment 8 with 12 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 16 points - only 0.00% unknown deleting segment 12 with 46 points - only 0.00% unknown deleting segment 13 with 28 points - only 0.00% unknown deleting segment 14 with 61 points - only 0.00% unknown deleting segment 15 with 14 points - only 0.00% unknown deleting segment 16 with 21 points - only 0.00% unknown deleting segment 17 with 32 points - only 0.00% unknown removing 3 vertex label from ripped group delemean absolute distance = 0.95 +- 1.28 5547 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... ting segment 18 with 3 points - only 0.00% unknown deleting segment 19 with 6 points - only 0.00% unknown deleting segment 20 with 14 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 21 with 3 points - only 0.00% unknown deleting segment 22 with 18 points - only 0.00% unknown deleting segment 23 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 24 with 3 points - only 0.00% unknown deleting segment 25 with 67 points - only 0.00% unknown deleting segment 26 with 5 points - only 0.00% unknown mean border=82.5, 146 (146) missing vertices, mean dist -0.1 [1.3 (%40.1)->0.7 (%59.9))] %67 local maxima, %25 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.89 +- 0.23 (0.04-->4.41) (max @ vno 54244 --> 54245) face area 0.29 +- 0.13 (0.00-->2.61) 000: dt: 0.0000, sse=3511937.8, rms=7.90 001: dt: 0.5000, sse=4448877.0, rms=5.28 002: dt: 0.5000, sse=4819973.5, rms=3.87 003: dt: 0.5000, sse=5197262.5, rms=3.25 004: dt: 0.5000, sse=5358986.0, rms=3.00 005: dt: 0.5000, sse=5506278.5, rms=2.93 rms = 2.90, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=5498546.5, rms=2.90 007: dt: 0.2500, sse=2941894.2, rms=1.87 008: dt: 0.2500, sse=2651931.0, rms=1.65 009: dt: 0.2500, sse=2529334.0, rms=1.60 rms = 1.57, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=2493666.0, rms=1.57 rms = 1.55, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=2458350.5, rms=1.55 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 247 points - only 8.91% 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 9 with 2 points - only 0.00% unknown deleting segment 10 with 34 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 13 with 744 points - only 0.00% unknown deleting segment 14 with 44 points - only 0.00% unknown deleting segment 15 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 18 with 105 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 19 with 4 points - only 0.00% unknown deleting segment 21 with 56 points - only 0.00% unknown deleting segment 22 with 22 points - only 0.00% unknown deleting segment 23 with 58 points - only 0.00% unknown deleting segment 24 with 15 points - only 0.00% unknown deleting segment 25 with 31 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 26 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 27 with 3 points - only 0.00% unknown deleting segment 28 with 6 points - only 0.00% unknown deleting segment 29mean absolute distance = 0.62 +- 1.11 6231 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... with 16 points - only 0.00% unknown deleting segment 30 with 78 points - only 0.00% unknown deleting segment 31 with 187 points - only 0.00% unknown mean border=84.2, 139 (35) missing vertices, mean dist -0.3 [0.8 (%59.5)->0.4 (%40.5))] %78 local maxima, %15 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 = 0.500 vertex spacing 0.88 +- 0.23 (0.12-->4.58) (max @ vno 54244 --> 54245) face area 0.33 +- 0.14 (0.00-->3.38) 000: dt: 0.0000, sse=2901440.5, rms=4.17 012: dt: 0.5000, sse=3243320.8, rms=2.62 013: dt: 0.5000, sse=3774601.0, rms=2.38 rms = 2.34, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=4011114.8, rms=2.34 015: dt: 0.2500, sse=2848212.2, rms=1.37 016: dt: 0.2500, sse=2681065.5, rms=1.15 rms = 1.11, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=2591362.8, rms=1.11 rms = 1.08, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=2556109.2, rms=1.08 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 257 points - only 8.95% unknown deleting segment 2 with 6 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 35 points - only 0.00% unknown deleting segment 5 with 730 points - only 0.00% unknown deleting segment 6 with 43 points - only 0.00% unknown deleting segment 7 with 9 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 87 points - only 0.00% unknown deleting segment 11 with 57 points - only 0.00% unknown deleting segment 12 with 25 points - only 0.00% unknown deleting segment 13 with 66 points - only 0.00% unknown deleting segment 14 with 15 points - only 0.00% unknown deleting segment 15 with 29 points - only 0.00% unknown deleting segment 16 with 21 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown deleting segment 18 with 6 points - only 0.00% unknown deleting segment 19 with 16 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 20 with 1 points - only 0.00% unknown deleting segment 21 with 74 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 22 with 3 points - only 0.00% unknown deleting segment 23 with 199 points - only 0.00% unknown mean border=85.0, 161 (23) missing vertices, meamean absolute distance = 0.49 +- 0.86 5321 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... n dist -0.2 [0.6 (%52.6)->0.3 (%47.4))] %84 local maxima, %10 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 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 = 0.250 vertex spacing 0.88 +- 0.23 (0.09-->4.59) (max @ vno 54244 --> 54245) face area 0.32 +- 0.14 (0.00-->3.40) 000: dt: 0.0000, sse=2673633.0, rms=2.49 019: dt: 0.5000, sse=2944785.5, rms=1.83 rms = 1.96, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=2740336.5, rms=1.37 021: dt: 0.2500, sse=2707704.2, rms=1.12 022: dt: 0.2500, sse=2674950.2, rms=1.06 rms = 1.04, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2658293.5, rms=1.04 rms = 1.02, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=2632585.2, rms=1.02 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 6 points - only 0.00% unknown deleting segment 1 with 258 points - only 8.91% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 7 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown deleting segment 5 with 36 points - only 0.00% unknown deleting segment 6 with 737 points - only 0.00% unknown deleting segment 7 with 42 points - only 0.00% unknown deleting segment 8 with 10 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 10 with 88 points - only 0.00% unknown deleting segment 12 with 71 points - only 0.00% unknown deleting segment 13 with 30 points - only 0.00% unknown deleting segment 14 with 74 points - only 0.00% unknown deleting segment 15 with 15 points - only 0.00% unknown deleting segment 16 with 29 points - only 0.00% unknown deleting segment 17 with 28 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 18 with 3 points - only 0.00% unknown deleting segment 19 with 6 points - only 0.00% unknown deleting segment 20 with 14 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 21 with 1 points - only 0.00% unknown deleting segment 22 with 74 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown deleting segment 24 with 197 points - only 0.00% mean absolute distance = 0.44 +- 0.73 4784 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... unknown mean border=85.3, 137 (18) missing vertices, mean dist -0.1 [0.6 (%47.5)->0.3 (%52.5))] %87 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 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 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=2697596.0, rms=1.92 025: dt: 0.5000, sse=3359854.2, rms=1.34 rms = 1.65, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3071098.2, rms=1.03 027: dt: 0.2500, sse=2965501.2, rms=0.92 rms = 0.87, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=2999413.0, rms=0.87 rms = 0.87, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=2994039.5, rms=0.87 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 47 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=59.8, 123 (123) missing vertices, mean dist 2.0 [0.0 (%0.0)->2.4 (%100.0))] %19 local maxima, %58 large gradients and %17 min vals, 2208 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 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 30 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=20264422.0, rms=26.58 001: dt: 0.5000, sse=15510299.0, rms=22.93 002: dt: 0.5000, sse=11946221.0, rms=19.78 003: dt: 0.5000, sse=9505326.0, rms=17.11 004: dt: 0.5000, sse=8047306.5, rms=14.80 005: dt: 0.5000, sse=7032749.5, rms=12.83 006: dt: 0.5000, sse=6262750.0, rms=11.16 007: dt: 0.5000, sse=5705647.0, rms=9.73 008: dt: 0.5000, sse=5272220.0, rms=8.48 009: dt: 0.5000, sse=4961569.5, rms=7.39 010: dt: 0.5000, sse=4735726.0, rms=6.44 011: dt: 0.5000, sse=4588611.5, rms=5.61 012: dt: 0.5000, sse=4466628.5, rms=4.90 013: dt: 0.5000, sse=4408025.0, rms=4.31 014: dt: 0.5000, sse=4336649.0, rms=3.81 015: dt: 0.5000, sse=4291125.5, rms=3.42 016: dt: 0.5000, sse=4255126.0, rms=3.11 017: dt: 0.5000, sse=4251869.5, rms=2.88 018: dt: 0.5000, sse=4244693.5, rms=2.69 019: dt: 0.5000, sse=4242198.5, rms=2.57 020: dt: 0.5000, sse=4229286.0, rms=2.46 021: dt: 0.5000, sse=4202278.0, rms=2.40 022: dt: 0.5000, sse=4227033.0, rms=2.34 rms = 2.31, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, ssesmoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... =4218791.5, rms=2.31 024: dt: 0.2500, sse=3034777.8, rms=1.93 025: dt: 0.2500, sse=2927329.5, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2885497.5, rms=1.85 rms = 1.83, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2834315.8, rms=1.83 positioning took 2.8 minutes mean border=56.8, 595 (51) missing vertices, mean dist 0.4 [0.3 (%39.1)->0.8 (%60.9))] %31 local maxima, %50 large gradients and %13 min vals, 1597 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 30 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 = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3678789.0, rms=5.13 028: dt: 0.5000, sse=3723571.2, rms=3.82 029: dt: 0.5000, sse=4173832.5, rms=3.10 030: dt: 0.5000, sse=4400055.0, rms=2.72 031: dt: 0.5000, sse=4545668.5, rms=2.51 032: dt: 0.5000, sse=4613280.5, rms=2.40 033: dt: 0.5000, sse=4684471.5, rms=2.35 rms = 2.31, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=4720494.0, rms=2.31 035: dt: 0.2500, sse=3629647.5, rms=1.93 036: dt: 0.2500, sse=3522484.0, rms=1.86 rms = 1.85, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=3470629.0, rms=1.85 rms = 1.83, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3420692.5, rms=1.83 positioning took 1.1 minutes mean border=55.8, 1079 (34) missing vertices, mean dist 0.2 [0.3 (%53.5)->0.7 (%46.5))] %46 local maxima, %36 large gradients and %12 min vals, 1033 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 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 30 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 = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3587447.5, rms=2.83 039: dt: 0.5000, sse=3827760.0, rms=2.23 040: dt: 0.5000, sse=4361703.5, rms=2.08 rms = 2.11, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=3892691.5, rms=1.88 042: dt: 0.2500, sse=3689866.0, rms=1.79 rms = 1.77, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=3655414.5, rms=1.77 rms = 1.75, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=3604846.2, rms=1.75 positioning took 0.7 minutes mean border=54.9, 2107 (31) missing vertices, mean dist 0.1 [0.3 (%49.4)->0.6 (%50.6))] %59 local maxima, %23 large gradients and %12 min vals, 1120 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 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 30 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 writing pial surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3679888.2, rms=2.38 045: dt: 0.5000, sse=3927339.5, rms=1.97 046: dt: 0.5000, sse=4287280.5, rms=1.85 rms = 1.96, time step reduction 1 of 3 to 0.250... 047: dt: 0.2500, sse=3947740.0, rms=1.69 048: dt: 0.2500, sse=3803175.2, rms=1.64 rms = 1.63, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=3762107.0, rms=1.63 rms = 1.62, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=3711985.0, rms=1.62 positioning took 0.7 minutes writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.area.pial vertex spacing 1.03 +- 0.42 (0.06-->7.78) (max @ vno 89886 --> 89874) face area 0.43 +- 0.30 (0.00-->7.01) measuring cortical thickness... 0 of 137427 vertices processed 25000 of 137427 vertices processed 50000 of 137427 vertices processed 75000 of 137427 vertices processed 100000 of 137427 vertices processed 125000 of 137427 vertices processed 0 of 137427 vertices processed 25000 of 137427 vertices processed 50000 of 137427 vertices processed 75000 of 137427 vertices processed 100000 of 137427 vertices processed 125000 of 137427 vertices processed thickness calculation complete, 3673:7804 truncations. 63805 vertices at 0 distance 78046 vertices at 1 distance 60968 vertices at 2 distance 31976 vertices at 3 distance 14871 vertices at 4 distance 6052 vertices at 5 distance 2390 vertices at 6 distance 1007 vertices at 7 distance 572 vertices at 8 distance 346 vertices at 9 distance 246 vertices at 10 distance 179 vertices at 11 distance 93 vertices at 12 distance 101 vertices at 13 distance 66 vertices at 14 distance 51 vertices at 15 distance 38 vertices at 16 distance 44 vertices at 17 distance 48 vertices at 18 distance 32 vertices at 19 distanwriting cortical thickness estimate to 'thickness' file. ce 45 vertices at 20 distance writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.thickness positioning took 11.8 minutes #-------------------------------------------- #@# Surf Volume lh Sat Mar 31 02:54:35 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 02:54:36 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts pctsurfcon --s cvs_avg35_inMNI152 --lh-only Log file is /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts/pctsurfcon.log Sat Mar 31 02:54:36 EDT 2012 setenv SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts /usr/local/freesurfer/dev/bin/pctsurfcon $Id: pctsurfcon,v 1.13 2011/11/10 20:21:13 nicks Exp $ Linux compute-0-104.local 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.wm.mgh --regheader cvs_avg35_inMNI152 --cortex srcvol = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz as target reference. Loading label /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label Reading surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 79475 Masking with /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.wm.mgh Dim: 137427 1 1 mri_vol2surf --mov /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.gm.mgh --projfrac 0.3 --regheader cvs_avg35_inMNI152 --cortex srcvol = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz as target reference. Loading label /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label Reading surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Done reading source surface Reading thickness /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 91098 Masking with /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.cortex.label Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.gm.mgh Dim: 137427 1 1 mri_concat /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.wm.mgh /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.8097/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.w-g.pct.mgh --annot cvs_avg35_inMNI152 lh aparc --sum /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.w-g.pct.mgh --annot cvs_avg35_inMNI152 lh aparc --sum /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/stats/lh.w-g.pct.stats --snr sysname Linux hostname compute-0-104.local machine x86_64 user lzollei 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.w-g.pct.mgh Vertex Area is 0.647793 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 9012 5840.24 1 1001 bankssts 1662 1103.68 2 1002 caudalanteriorcingulate 905 566.15 3 1003 caudalmiddlefrontal 4126 2673.6 4 1004 corpuscallosum 0 5 1005 cuneus 2012 1355.05 6 1006 entorhinal 597 363.185 7 1007 fusiform 4901 3083.53 8 1008 inferiorparietal 6843 4472.65 9 1009 inferiortemporal 5542 3576.19 10 1010 isthmuscingulate 1488 964.228 11 1011 lateraloccipital 7523 4917.71 12 1012 lateralorbitofrontal 3628 2308.86 13 1013 lingual 4018 2551.82 14 1014 medialorbitofrontal 2778 1892.03 15 1015 middletemporal 4428 2882.37 16 1016 parahippocampal 1173 741.069 17 1017 paracentral 2214 1442.51 18 1018 parsopercularis 2466 1593.57 19 1019 parsorbitalis 812 479.104 20 1020 parstriangularis 1828 1168.42 21 1021 pericalcarine 1735 1189.63 22 1022 postcentral 7063 4641.02 23 1023 posteriorcingulate 1772 1167.94 24 1024 precentral 8679 5581 25 1025 precuneus 5650 3677.72 26 1026 rostralanteriorcingulate 1142 723.65 27 1027 rostralmiddlefrontal 7924 4944.85 28 1028 superiorfrontal 10255 6728.85 29 1029 superiorparietal 8594 5529.8 30 1030 superiortemporal 5956 3835.68 31 1031 supramarginal 5942 3896.45 32 1032 frontalpole 252 145.637 33 1033 temporalpole 676 417.024 34 1034 transversetemporal 668 424.276 35 1035 insula 3163 2143.99 Reporting on 35 segmentations Cleaning up #----------------------------------------- #@# Parcellation Stats lh Sat Mar 31 02:54:45 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 cvs_avg35_inMNI152 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1662 1104 2371 2.043 0.779 0.075 0.013 5 0.9 bankssts 905 566 1493 2.160 0.807 0.128 0.029 11 1.1 caudalanteriorcingulate 4126 2674 7254 2.334 0.768 0.126 0.041 43 7.1 caudalmiddlefrontal 2012 1355 4176 2.715 0.897 0.135 0.040 20 3.5 cuneus 597 363 2196 3.555 1.215 0.106 0.023 5 0.6 entorhinal 4901 3084 11891 3.161 0.980 0.135 0.063 101 12.7 fusiform 6843 4473 13663 2.611 0.944 0.123 0.041 72 11.6 inferiorparietal 5542 3576 15172 3.250 1.105 0.129 0.042 62 9.6 inferiortemporal 1488 964 2922 2.670 1.023 0.121 0.039 16 2.2 isthmuscingulate 7523 4918 15030 2.825 0.766 0.139 0.044 85 14.1 lateraloccipital 3628 2309 8835 2.958 1.182 0.110 0.036 35 5.6 lateralorbitofrontal 4018 2552 8577 2.838 0.870 0.136 0.087 78 7.8 lingual 2778 1892 6080 2.712 1.066 0.115 0.050 39 4.3 medialorbitofrontal 4428 2882 12024 2.978 1.128 0.119 0.037 46 6.9 middletemporal 1173 741 1637 1.960 0.686 0.075 0.013 4 0.6 parahippocampal 2214 1443 3860 2.281 0.844 0.110 0.031 15 2.8 paracentral 2466 1594 5257 2.537 0.902 0.114 0.035 25 3.7 parsopercularis 812 479 2400 3.256 1.160 0.136 0.051 12 1.7 parsorbitalis 1828 1168 4237 2.570 1.096 0.134 0.050 24 3.7 parstriangularis 1735 1190 2802 2.602 0.804 0.130 0.373 44 3.0 pericalcarine 7063 4641 10803 1.991 0.836 0.120 0.038 84 11.9 postcentral 1772 1168 2814 2.130 0.922 0.139 0.083 80 3.6 posteriorcingulate 8679 5581 14451 2.297 0.808 0.117 0.044 88 15.6 precentral 5650 3678 11261 2.501 1.062 0.127 0.052 87 12.3 precuneus 1142 724 1728 2.056 0.805 0.119 0.031 13 1.5 rostralanteriorcingulate 7924 4945 16547 2.531 1.034 0.135 0.055 105 19.0 rostralmiddlefrontal 10255 6729 24355 2.836 1.111 0.118 0.037 91 15.9 superiorfrontal 8594 5530 14192 2.258 0.860 0.127 0.066 200 20.8 superiorparietal 5956 3836 12903 2.760 1.005 0.097 0.024 36 6.2 superiortemporal 5942 3896 11826 2.557 0.954 0.134 0.043 71 11.1 supramarginal 252 146 793 3.383 0.899 0.151 0.101 7 0.8 frontalpole 676 417 3035 3.959 0.821 0.111 0.033 7 1.1 temporalpole 668 424 1168 2.544 0.870 0.125 0.036 7 0.9 transversetemporal 3163 2144 6883 2.814 1.304 0.081 0.018 14 2.2 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Mar 31 02:55:01 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 cvs_avg35_inMNI152 lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 45 labels changed using aseg relabeling using gibbs priors... 000: 8771 changed, 137427 examined... 001: 1954 changed, 33384 examined... 002: 627 changed, 10166 examined... 003: 235 changed, 3471 examined... 004: 107 changed, 1336 examined... 005: 53 changed, 616 examined... 006: 29 changed, 291 examined... 007: 10 changed, 162 examined... 008: 7 changed, 55 examined... 009: 5 changed, 38 examined... 010: 5 changed, 21 examined... 011: 3 changed, 23 examined... 012: 1 changed, 11 examined... 013: 0 changed, 7 examined... 10 labels changed using aseg 000: 250 total segments, 168 labels (1937 vertices) changed 001: 97 total segments, 15 labels (50 vertices) changed 002: 83 total segments, 1 labels (1 vertices) changed 003: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 108 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 949 vertices marked for relabeling... 949 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 58 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Mar 31 02:55:59 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 cvs_avg35_inMNI152 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1034 630 2250 2.568 1.171 0.135 0.057 14 2.5 G_and_S_frontomargin 2090 1378 4636 3.104 0.731 0.143 0.049 23 4.4 G_and_S_occipital_inf 1734 1151 3173 2.299 0.611 0.122 0.035 13 2.6 G_and_S_paracentral 1350 880 3160 2.649 0.955 0.133 0.043 18 2.4 G_and_S_subcentral 668 404 1819 3.113 0.725 0.146 0.063 10 1.7 G_and_S_transv_frontopol 2497 1595 4670 2.351 1.047 0.120 0.033 25 3.6 G_and_S_cingul-Ant 1073 705 1805 2.157 0.846 0.111 0.026 9 1.2 G_and_S_cingul-Mid-Ant 1476 936 2556 2.281 1.003 0.130 0.098 76 3.5 G_and_S_cingul-Mid-Post 371 250 1170 3.375 0.761 0.154 0.054 5 0.8 G_cingul-Post-dorsal 373 225 734 2.923 0.974 0.137 0.051 5 0.7 G_cingul-Post-ventral 1800 1233 3990 2.704 0.841 0.143 0.044 20 3.3 G_cuneus 1565 972 4199 2.903 0.835 0.137 0.046 24 3.3 G_front_inf-Opercular 359 211 1186 3.487 0.954 0.186 0.086 11 1.1 G_front_inf-Orbital 1102 701 3360 3.046 0.992 0.142 0.056 15 2.7 G_front_inf-Triangul 4853 3020 12083 2.798 0.901 0.139 0.054 68 11.6 G_front_middle 6811 4485 19258 3.205 0.965 0.123 0.038 62 10.9 G_front_sup 439 304 1407 3.542 1.151 0.113 0.039 5 0.6 G_Ins_lg_and_S_cent_ins 633 412 2453 3.939 0.999 0.071 0.017 2 0.5 G_insular_short 2328 1484 6078 3.084 0.740 0.149 0.052 34 5.0 G_occipital_middle 1701 1132 3592 2.891 0.856 0.147 0.060 23 3.5 G_occipital_sup 1905 1177 5077 3.235 0.781 0.133 0.045 28 3.8 G_oc-temp_lat-fusifor 2725 1687 6635 2.997 0.760 0.144 0.051 39 6.0 G_oc-temp_med-Lingual 1059 665 2362 2.496 1.051 0.087 0.015 5 0.7 G_oc-temp_med-Parahip 2330 1439 7635 3.510 0.936 0.136 0.053 36 5.5 G_orbital 2688 1721 6924 3.099 0.832 0.140 0.049 35 5.5 G_pariet_inf-Angular 2914 1901 7167 2.924 0.878 0.150 0.054 47 6.6 G_pariet_inf-Supramar 3277 2082 6852 2.575 0.823 0.130 0.043 35 6.3 G_parietal_sup 2860 1853 4480 1.991 0.731 0.118 0.035 29 4.4 G_postcentral 3292 2101 6550 2.448 0.777 0.114 0.035 27 4.8 G_precentral 2630 1701 7008 2.882 1.029 0.146 0.054 48 6.4 G_precuneus 1035 729 2804 2.810 1.038 0.164 0.114 34 3.2 G_rectus 302 193 704 3.314 1.117 0.079 0.021 2 0.2 G_subcallosal 447 281 915 2.595 0.692 0.119 0.031 4 0.5 G_temp_sup-G_T_transv 2112 1366 6856 3.348 0.916 0.125 0.034 21 3.0 G_temp_sup-Lateral 726 472 1775 3.120 0.856 0.055 0.010 1 0.3 G_temp_sup-Plan_polar 1009 655 2102 2.770 0.913 0.092 0.026 7 1.1 G_temp_sup-Plan_tempo 2858 1815 10153 3.758 0.875 0.141 0.050 37 6.0 G_temporal_inf 2752 1765 9657 3.446 1.027 0.129 0.043 33 5.0 G_temporal_middle 266 173 441 2.289 0.783 0.118 0.035 2 0.3 Lat_Fis-ant-Horizont 301 192 499 2.369 0.778 0.123 0.042 3 0.5 Lat_Fis-ant-Vertical 1279 847 1528 1.967 0.714 0.090 0.020 5 1.0 Lat_Fis-post 1927 1243 3472 2.408 0.687 0.141 0.044 26 3.5 Pole_occipital 1705 1059 7091 3.786 1.117 0.134 0.048 22 3.5 Pole_temporal 2340 1555 3475 2.398 0.962 0.124 0.371 80 5.1 S_calcarine 3552 2348 3586 1.691 0.535 0.101 0.025 18 3.9 S_central 1232 808 1502 1.779 0.810 0.092 0.019 5 1.2 S_cingul-Marginalis 545 351 714 2.101 0.737 0.066 0.012 1 0.3 S_circular_insula_ant 1617 1036 2173 2.372 1.114 0.068 0.011 4 0.8 S_circular_insula_inf 1854 1252 1954 1.649 0.569 0.083 0.015 6 1.2 S_circular_insula_sup 1053 667 2169 3.263 1.175 0.132 0.095 39 4.3 S_collat_transv_ant 376 252 656 2.976 0.476 0.131 0.035 3 0.6 S_collat_transv_post 2038 1311 2653 1.866 0.624 0.124 0.043 23 3.5 S_front_inf 1484 1010 2257 2.296 0.991 0.119 0.036 10 2.4 S_front_middle 3126 2020 4439 2.040 0.917 0.116 0.046 31 6.0 S_front_sup 327 229 421 2.145 0.862 0.128 0.034 2 0.5 S_interm_prim-Jensen 2933 1901 3646 1.913 0.693 0.106 0.029 19 3.7 S_intrapariet_and_P_trans 1250 836 2185 2.899 0.745 0.123 0.039 9 2.1 S_oc_middle_and_Lunatus 1334 923 1776 2.333 0.793 0.107 0.030 7 1.6 S_oc_sup_and_transversal 1086 713 2078 2.560 1.035 0.122 0.034 10 1.6 S_occipital_ant 980 613 1600 2.962 0.837 0.116 0.038 11 1.4 S_oc-temp_lat 2215 1445 3207 2.464 1.019 0.118 0.051 36 3.4 S_oc-temp_med_and_Lingual 330 208 364 1.725 0.501 0.100 0.027 1 0.3 S_orbital_lateral 957 661 1840 2.709 1.178 0.085 0.016 4 0.6 S_orbital_med-olfact 1254 791 2352 2.604 1.211 0.095 0.027 7 1.4 S_orbital-H_Shaped 1977 1324 3125 2.412 0.964 0.115 0.042 21 3.7 S_parieto_occipital 1405 883 1407 2.014 0.616 0.113 0.025 16 1.3 S_pericallosal 3765 2433 4789 1.971 0.873 0.138 0.104 174 14.4 S_postcentral 1573 991 2492 2.535 0.721 0.127 0.090 31 5.0 S_precentral-inf-part 1710 1173 2223 2.110 0.713 0.111 0.029 11 2.3 S_precentral-sup-part 516 351 975 2.458 0.837 0.084 0.014 2 0.3 S_suborbital 1062 677 1351 1.800 0.796 0.102 0.027 6 1.1 S_subparietal 1687 1135 2323 2.240 0.739 0.112 0.027 13 1.9 S_temporal_inf 5759 3789 7842 2.078 0.763 0.092 0.024 32 5.9 S_temporal_sup 422 273 801 3.591 0.644 0.139 0.039 5 0.8 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Sat Mar 31 02:56:17 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 4 found - 4 modified | TOTAL: 7 pass 2 (yz+): 0 found - 4 modified | TOTAL: 7 pass 1 (yz-): 1 found - 1 modified | TOTAL: 8 pass 2 (yz-): 0 found - 1 modified | TOTAL: 8 pass 1 (xz+): 1 found - 1 modified | TOTAL: 9 pass 2 (xz+): 0 found - 1 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 0 found - 0 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 = 12 (out of 346213: 0.003466) 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 1.721 2012/03/08 13:49:42 fischl Exp $ slice 50: 1401 vertices, 1493 faces slice 60: 5983 vertices, 6162 faces slice 70: 12651 vertices, 12914 faces slice 80: 21081 vertices, 21400 faces slice 90: 30061 vertices, 30430 faces slice 100: 40003 vertices, 40313 faces slice 110: 50405 vertices, 50705 faces slice 120: 62406 vertices, 62762 faces slice 130: 73658 vertices, 74051 faces slice 140: 85193 vertices, 85572 faces slice 150: 95706 vertices, 96079 faces slice 160: 104721 vertices, 104995 faces slice 170: 112169 vertices, 112423 faces slice 180: 119049 vertices, 119267 faces slice 190: 124899 vertices, 125083 faces slice 200: 129915 vertices, 130092 faces slice 210: 133520 vertices, 133602 faces slice 220: 134188 vertices, 134190 faces slice 230: 134188 vertices, 134190 faces slice 240: 134188 vertices, 134190 faces slice 250: 134188 vertices, 134190 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... 134188 voxel in cpt #1: X=-2 [v=134188,e=402570,f=268380] located at (31.485729, -3.695070, -1.745625) For the whole surface: X=-2 [v=134188,e=402570,f=268380] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat Mar 31 02:56:27 EDT 2012 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 02:56:32 EDT 2012 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 49.6 mm, total surface area = 76248 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.8 minutes step 000: RMS=0.083 (target=0.015) step 005: RMS=0.062 (target=0.015) step 010: RMS=0.047 (target=0.015) step 015: RMS=0.038 (target=0.015) step 020: RMS=0.033 (target=0.015) step 025: RMS=0.029 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.022 (target=0.015) step 045: RMS=0.020 (target=0.015) step 050: RMS=0.019 (target=0.015) step 055: RMS=0.018 (target=0.015) step 060: RMS=0.018 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sat Mar 31 02:57:18 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading original vertex positions... unfolding cortex into spherical form... scaling brain by 0.312... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.585, avgs=0 005/300: dt: 0.9000, rms radial error=176.325, avgs=0 010/300: dt: 0.9000, rms radial error=175.767, avgs=0 015/300: dt: 0.9000, rms radial error=175.034, avgs=0 020/300: dt: 0.9000, rms radial error=174.199, avgs=0 025/300: dt: 0.9000, rms radial error=173.305, avgs=0 030/300: dt: 0.9000, rms radial error=172.378, avgs=0 035/300: dt: 0.9000, rms radial error=171.441, avgs=0 040/300: dt: 0.9000, rms radial error=170.500, avgs=0 045/300: dt: 0.9000, rms radial error=169.556, avgs=0 050/300: dt: 0.9000, rms radial error=168.614, avgs=0 055/300: dt: 0.9000, rms radial error=167.673, avgs=0 060/300: dt: 0.9000, rms radial error=166.736, avgs=0 065/300: dt: 0.9000, rms radial error=165.803, avgs=0 070/300: dt: 0.9000, rms radial error=164.875, avgs=0 075/300: dt: 0.9000, rms radial error=163.951, avgs=0 080/300: dt: 0.9000, rms radial error=163.032, avgs=0 085/300: dt: 0.9000, rms radial error=162.118, avgs=0 090/300: dt: 0.9000, rms radial error=161.209, avgs=0 095/300: dt: 0.9000, rms radial error=160.305, avgs=0 100/300: dt: 0.9000, rms radial error=159.406, avgs=0 105/300: dt: 0.9000, rms radial error=158.512, avgs=0 110/300: dt: 0.9000, rms radial error=157.622, avgs=0 115/300: dt: 0.9000, rms radial error=156.738, avgs=0 120/300: dt: 0.9000, rms radial error=155.858, avgs=0 125/300: dt: 0.9000, rms radial error=154.983, avgs=0 130/300: dt: 0.9000, rms radial error=154.114, avgs=0 135/300: dt: 0.9000, rms radial error=153.248, avgs=0 140/300: dt: 0.9000, rms radial error=152.388, avgs=0 145/300: dt: 0.9000, rms radial error=151.532, avgs=0 150/300: dt: 0.9000, rms radial error=150.683, avgs=0 155/300: dt: 0.9000, rms radial error=149.838, avgs=0 160/300: dt: 0.9000, rms radial error=148.998, avgs=0 165/300: dt: 0.9000, rms radial error=148.163, avgs=0 170/300: dt: 0.9000, rms radial error=147.332, avgs=0 175/300: dt: 0.9000, rms radial error=146.505, avgs=0 180/300: dt: 0.9000, rms radial error=145.683, avgs=0 185/300: dt: 0.9000, rms radial error=144.865, avgs=0 190/300: dt: 0.9000, rms radial error=144.052, avgs=0 195/300: dt: 0.9000, rms radial error=143.244, avgs=0 200/300: dt: 0.9000, rms radial error=142.439, avgs=0 205/300: dt: 0.9000, rms radial error=141.640, avgs=0 210/300: dt: 0.9000, rms radial error=140.844, avgs=0 215/300: dt: 0.9000, rms radial error=140.053, avgs=0 220/300: dt: 0.9000, rms radial error=139.266, avgs=0 225/300: dt: 0.9000, rms radial error=138.483, avgs=0 230/300: dt: 0.9000, rms radial error=137.705, avgs=0 235/300: dt: 0.9000, rms radial error=136.931, avgs=0 240/300: dt: 0.9000, rms radial error=136.162, avgs=0 245/300: dt: 0.9000, rms radial error=135.396, avgs=0 250/300: dt: 0.9000, rms radial error=134.635, avgs=0 255/300: dt: 0.9000, rms radial error=133.878, avgs=0 260/300: dt: 0.9000, rms radial error=133.125, avgs=0 265/300: dt: 0.9000, rms radial error=132.376, avgs=0 270/300: dt: 0.9000, rms radial error=131.632, avgs=0 275/300: dt: 0.9000, rms radial error=130surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.54 (0.00-->6.82) (max @ vno 53874 --> 53882) face area 0.03 +- 0.03 (-0.02-->0.80) .891, avgs=0 280/300: dt: 0.9000, rms radial error=130.155, avgs=0 285/300: dt: 0.9000, rms radial error=129.423, avgs=0 290/300: dt: 0.9000, rms radial error=128.695, avgs=0 295/300: dt: 0.9000, rms radial error=127.971, avgs=0 300/300: dt: 0.9000, rms radial error=127.251, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15420.89 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 = 2441.15 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 = 214.03 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.15/15 = 0.01032 epoch 4 (K=640.0), pass 1, starting sse = 7.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.38/20 = 0.01914 final dwriting spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.11 hours istance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat Mar 31 03:03:42 EDT 2012 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 cvs_avg35_inMNI152 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 1.721 2012/03/08 13:49:42 fischl Exp $ before topology correction, eno=-2 (nv=134188, nf=268380, ne=402570, g=2) 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 10 iterations marking ambiguous vertices... 1092 ambiguous faces found in tessellation segmenting defects... 10 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 10 defects to be corrected 0 vertices coincident reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.9538 (-4.4769) -vertex loglikelihood: -5.9727 (-2.9864) -normal dot loglikelihood: -3.6596 (-3.6596) -quad curv loglikelihood: -6.1825 (-3.0913) Total Loglikelihood : -24.7686 CORRECTING DEFECT 0 (vertices=164, convex hull=77) After retessellation of defect 0, euler #=-7 (133553,400504,266944) : difference with theory (-7) = 0 CORRECTING DEFECT 1 (vertices=6, convex hull=31) After retessellation of defect 1, euler #=-6 (133556,400521,266959) : difference with theory (-6) = 0 CORRECTING DEFECT 2 (vertices=132, convex hull=106) After retessellation of defect 2, euler #=-5 (133597,400692,267090) : difference with theory (-5) = 0 CORRECTING DEFECT 3 (vertices=14, convex hull=35) After retessellation of defect 3, euler #=-4 (133600,400711,267107) : difference with theory (-4) = 0 CORRECTING DEFECT 4 (vertices=30, convex hull=35) After retessellation of defect 4, euler #=-3 (133604,400734,267127) : difference with theory (-3) = 0 CORRECTING DEFECT 5 (vertices=10, convex hull=15) After retessellation of defect 5, euler #=-2 (133606,400743,267135) : difference with theory (-2) = 0 CORRECTING DEFECT 6 (vertices=8, convex hull=20) After retessellation of defect 6, euler #=-1 (133607,400753,267145) : difference with theory (-1) = 0 CORRECTING DEFECT 7 (vertices=219, convex hull=42) After retessellation of defect 7, euler #=0 (133619,400806,267187) : difference with theory (0) = 0 CORRECTING DEFECT 8 (vertices=38, convex hull=56) After retessellation of defect 8, euler #=1 (133641,400893,267253) : difference with theory (1) = 0 CORRECTING DEFECT 9 (vertices=27, convex hull=54) After retessellation of defect 9, euler #=2 (133655,400959,267306) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.21 (0.04-->5.21) (max @ vno 32781 --> 33864) 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 (0.04-->5.21) (max @ vno 32781 --> 33864) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 26 mutations (36.1%), 46 crossovers (63.9%), 12 vertices were eliminated building final representation... 533 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=133655, nf=267306, ne=400959, g=0) writing corrected surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 5.3 minutes 0 defective edges removing intersecting faces 000: 66 intersecting 001: 4 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 133655 - 400959 + 267306 = 2 --> 0 holes F =2V-4: 267306 = 267310-4 (0) 2E=3F: 801918 = 801918 (0) total defect index = 0 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 24 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Mar 31 03:09:07 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs cvs_avg35_inMNI152 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 1.130 2011/12/08 15:01:24 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/filled.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/brain.finalsurfs.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... 5036 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.orig... computing class statistics... border white: 261470 voxels (1.56%) border gray 278696 voxels (1.66%) WM (94.0): 94.6 +- 7.0 [70.0 --> 110.0] GM (83.0) : 80.4 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.7 (was 70) setting MAX_BORDER_WHITE to 108.0 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 45.3 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.84 +- 0.21 (0.01-->3.16) (max @ vno 33864 --> 133586) face area 0.30 +- 0.12 (0.00-->1.90) mean absolute distance = 0.90 +- 1.21 4975 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=68 using class modes intead of means.... mean inside = 92.5, mean outside = 76.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.9, 103 (103) missing vertices, mean dist -0.0 [1.2 (%37.7)->0.7 (%62.3))] %69 local maxima, %22 large gradients and % 3 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 0.89 +- 0.23 (0.07-->3.64) (max @ vno 94824 --> 94832) face area 0.30 +- 0.13 (0.00-->1.90) mean absolute distance = 0.60 +- 1.08 5694 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3327065.0, rms=7.92 001: dt: 0.5000, sse=4283227.5, rms=5.33 002: dt: 0.5000, sse=4670972.5, rms=3.91 003: dt: 0.5000, sse=5094580.5, rms=3.26 004: dt: 0.5000, sse=5240106.5, rms=3.02 005: dt: 0.5000, sse=5414356.0, rms=2.95 rms = 2.92, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=5408023.0, rms=2.92 007: dt: 0.2500, sse=2864241.0, rms=1.76 008: dt: 0.2500, sse=2564454.5, rms=1.51 009: dt: 0.2500, sse=2440378.5, rms=1.45 rms = 1.42, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=2406726.2, rms=1.42 rms = 1.39, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=2365861.2, rms=1.39 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=83.7, 20 (6) missing vertices, mean dist -0.3 [0.7 (%60.0)->0.4 (%40.0))] %79 local maxima, %13 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 = 0.500 vertex spacing 0.88 +- 0.23 (0.07-->3.43) (max @ vno 133586 --> 133583) face area 0.33 +- 0.15 (0.00-->2.59) mean absolute distance = 0.48 +- 0.83 5244 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2771968.5, rms=4.06 012: dt: 0.5000, sse=3093087.0, rms=2.56 013: dt: 0.5000, sse=3615584.2, rms=2.42 rms = 2.40, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=3808475.5, rms=2.40 015: dt: 0.2500, sse=2710936.8, rms=1.34 016: dt: 0.2500, sse=2550591.5, rms=1.10 rms = 1.06, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=2467029.2, rms=1.06 rms = 1.02, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=2430783.0, rms=1.02 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.5, 21 (2) missing vertices, mean dist -0.2 [0.6 (%52.9)->0.3 (%47.1))] %84 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 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 = 0.250 vertex spacing 0.88 +- 0.23 (0.11-->3.56) (max @ vno 133586 --> 133583) face area 0.33 +- 0.14 (0.00-->2.56) mean absolute distance = 0.43 +- 0.73 4319 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=2555803.8, rms=2.54 019: dt: 0.5000, sse=2830800.0, rms=1.91 rms = 2.06, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=2634172.0, rms=1.40 021: dt: 0.2500, sse=2607649.2, rms=1.13 022: dt: 0.2500, sse=2571058.0, rms=1.05 rms = 1.02, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2559762.2, rms=1.02 rms = 1.00, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=2539078.0, rms=1.00 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=84.7, 16 (0) missing vertices, mean dist -0.1 [0.5 (%48.1)->0.3 (%51.9))] %86 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 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 writing white matter surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... 000: dt: 0.0000, sse=2604600.5, rms=1.90 025: dt: 0.5000, sse=3268902.0, rms=1.36 rms = 1.73, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=2977910.8, rms=1.00 027: dt: 0.2500, sse=2870804.5, rms=0.89 rms = 0.85, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=2903037.8, rms=0.85 rms = 0.84, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=2896814.5, rms=0.84 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2356 vertices erasing segment 1 (vno[0] = 48726) erasing segment 2 (vno[0] = 77565) erasing segment 3 (vno[0] = 79926) erasing segment 4 (vno[0] = 82216) erasing segment 5 (vno[0] = 84404) erasing segment 6 (vno[0] = 88658) erasing segment 7 (vno[0] = 94824) erasing segment 8 (vno[0] = 94954) erasing segment 9 (vno[0] = 99192) erasing segment 10 (vno[0] = 100873) erasing segment 11 (vno[0] = 101646) erasing segment 12 (vno[0] = 102378) erasing sewriting smoothed curvature to rh.curv gment 13 (vno[0] = 103865) erasing segment 14 (vno[0] = 103873) erasing segment 15 (vno[0] = 104637) erasing segment 16 (vno[0] = 104640) erasing segment 17 (vno[0] = 105321) erasing segment 18 (vno[0] = 105346) writing cortex label to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label... LabelWrite: saving to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.area vertex spacing 0.89 +- 0.23 (0.10-->3.64) (max @ vno 94824 --> 94832) face area 0.33 +- 0.14 (0.00-->2.85) refinement took 5.0 minutes #-------------------------------------------- #@# Smooth2 rh Sat Mar 31 03:14:05 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 03:14:10 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 49.7 mm, total surface area = 82066 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.096 (target=0.015) step 005: RMS=0.067 (target=0.015) step 010: RMS=0.049 (target=0.015) step 015: RMS=0.040 (target=0.015) step 020: RMS=0.034 (target=0.015) step 025: RMS=0.028 (target=0.015) step 030: RMS=0.025 (target=0.015) step 035: RMS=0.021 (target=0.015) step 040: RMS=0.019 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 0.7 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 273 vertices thresholded to be in k1 ~ [-0.31 0.34], k2 ~ [-0.10 0.06] total integrated curvature = 0.522*4pi (6.555) --> 0 handles ICI = 1.7, FI = 13.2, variation=217.678 151 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 137 vertices thresholded to be in [-0.16 0.18] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.028 done. #----------------------------------------- #@# Curvature Stats rh Sat Mar 31 03:16:20 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm cvs_avg35_inMNI152 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 [ cvs_avg35_inMNI152/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 [ 270 ] Gb_filter = 0 WARN: S lookup min: -0.128900 WARN: S explicit min: 0.000000 vertex = 53 #-------------------------------------------- #@# Sphere rh Sat Mar 31 03:16:27 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1.721 2012/03/08 13:49:42 fischl 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=compu, 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 %19.14 pass 1: epoch 2 of 3 starting distance error %19.12 unfolding complete - removing small folds... starting distance error %19.07 removing remaining folds... final distance error %19.09 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.87 hours #-------------------------------------------- #@# Surf Reg rh Sat Mar 31 04:08:25 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.60 2011/09/20 17:53:32 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/dev/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=compu, 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=compu, 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 -------------------- 1 Reading rh.sulc curvature mean = -0.000, std = 0.623 curvature mean = 0.045, std = 0.925 curvature mean = 0.010, std = 0.878 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 16.00) sse = 350150.6, tmin=1.2957 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 245008.5, tmin=2.6454 d=16.00 min @ (4.00, 0.00, 4.00) sse = 212275.0, tmin=4.0120 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 208735.8, tmin=6.6723 d=2.00 min @ (0.00, -0.50, 0.00) sse = 207896.3, tmin=8.0572 d=1.00 min @ (0.00, 0.00, -0.25) sse = 207894.1, tmin=9.4498 d=0.50 min @ (0.00, 0.00, 0.12) sse = 207871.8, tmin=10.8449 tol=1.0e+00, sigma=0.5, host=compu, 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 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 MRISrigidBodyAlignGlobal() done 10.84 min curvature mean = 0.032, std = 0.947 curvature mean = 0.003, std = 0.955 curvature mean = 0.031, std = 0.961 curvature mean = 0.001, std = 0.982 curvature mean = 0.030, std = 0.963 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.024, std = 0.209 curvature mean = 0.007, std = 0.070 curvature mean = 0.037, std = 0.459 curvature mean = 0.007, std = 0.085 curvature mean = 0.020, std = 0.652 curvature mean = 0.007, std = 0.092 curvature mean = 0.010, std = 0.788 curvature mean = 0.007, std = 0.095 curvature mean = 0.002, std = 0.880 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat Mar 31 05:16:58 EDT 2012 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 Sat Mar 31 05:17:00 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/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/dev/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Sat Mar 31 05:17:03 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 cvs_avg35_inMNI152 rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 1167 labels changed using aseg relabeling using gibbs priors... 000: 2879 changed, 133655 examined... 001: 680 changed, 12222 examined... 002: 127 changed, 3846 examined... 003: 42 changed, 778 examined... 004: 21 changed, 251 examined... 005: 4 changed, 116 examined... 006: 2 changed, 26 examined... 007: 1 changed, 15 examined... 008: 1 changed, 7 examined... 009: 2 changed, 7 examined... 010: 1 changed, 10 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 1 changed, 6 examined... 014: 0 changed, 8 examined... 127 labels changed using aseg 000: 101 total segments, 62 labels (353 vertices) changed 001: 40 total segments, 1 labels (14 vertices) changed 002: 39 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 49 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 809 vertices marked for relabeling... 809 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 51 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat Mar 31 05:17:53 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs cvs_avg35_inMNI152 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 1.130 2011/12/08 15:01:24 fischl Exp $ $Id: mrisurf.c,v 1.721 2012/03/08 13:49:42 fischl Exp $ reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/filled.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/brain.finalsurfs.mgz... reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... 5036 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.orig... computing class statistics... border white: 261470 voxels (1.56%) border gray 278696 voxels (1.66%) WM (94.0): 94.6 +- 7.0 [70.0 --> 110.0] GM (83.0) : 80.4 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 56.7 (was 70) setting MAX_BORDER_WHITE to 108.0 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 45.3 (was 40) setting MAX_GRAY to 94.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.3 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 34.0 (was 40) smoothing contralateral hemisphere... intensity peaks found at WM=101, GM=68 using class modes intead of means.... mean inside = 92.5, mean outside = 76.4 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.84 +- 0.21 (0.01-->3.16) (max @ vno 33864 --> 133586) face area 0.30 +- 0.12 (0.00-->1.90) inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group deleting segment 0 with 4 points - only 0.00% unknown deleting segment 1 with 71 points - only 0.00% unknown deleting segment 2 with 40 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown deleting segment 5 with 5 points - only 0.00% unknown deleting segment 6 with 14 points - only 0.00% unknown deleting segment 7 with 20 points - only 0.00% unknown deleting segment 8 with 634 points - only 0.00% unknown deleting segment 10 with 5 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 7 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown deleting segment 14 with 64 points - only 0.00% unknown mean border=82.0, 103 (103) missing vertices, mean dist -0.0 [1.2 (%37.9)->0.7 (%62.1))] %70 local maxima, %22 large gradients and % 3 min vals, 0 gradients ignoredmean absolute distance = 0.91 +- 1.24 5139 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tol=1.0e-04, sigma=2.0, host=compu, 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 0.89 +- 0.23 (0.07-->3.64) (max @ vno 94824 --> 94832) face area 0.30 +- 0.13 (0.00-->2.35) 000: dt: 0.0000, sse=3355767.0, rms=7.95 001: dt: 0.5000, sse=4309896.0, rms=5.36 002: dt: 0.5000, sse=4693058.0, rms=3.93 003: dt: 0.5000, sse=5118577.0, rms=3.28 004: dt: 0.5000, sse=5259925.0, rms=3.03 005: dt: 0.5000, sse=5439026.0, rms=2.96 rms = 2.92, time step reduction 1 of 3 to 0.250... 006: dt: 0.5000, sse=5427958.5, rms=2.92 007: dt: 0.2500, sse=2874346.0, rms=1.77 008: dt: 0.2500, sse=2573045.2, rms=1.52 009: dt: 0.2500, sse=2446829.8, rms=1.45 rms = 1.42, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=2412685.2, rms=1.42 rms = 1.40, time step reduction 3 of 3 to 0.062... 011: dt: 0.1250, sse=2372561.8, rms=1.40 positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 91 points - only 0.00% unknown deleting segment 2 with 43 points - only 0.00% unknown deleting segment 3 with 15 points - only 0.00% unknown deleting segment 4 with 20 points - only 0.00% unknown removing 2 vermean absolute distance = 0.60 +- 1.10 5892 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... tex label from ripped group deleting segment 8 with 5 points - only 0.00% unknown deleting segment 9 with 34 points - only 0.00% unknown deleting segment 11 with 8 points - only 0.00% unknown deleting segment 12 with 694 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown deleting segment 14 with 6 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 4 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 17 with 3 points - only 0.00% unknown deleting segment 18 with 68 points - only 0.00% unknown mean border=83.7, 29 (6) missing vertices, mean dist -0.3 [0.7 (%59.8)->0.4 (%40.2))] %80 local maxima, %13 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 = 0.500 vertex spacing 0.88 +- 0.23 (0.07-->2.93) (max @ vno 84580 --> 83514) face area 0.33 +- 0.14 (0.00-->2.40) 000: dt: 0.0000, sse=2803629.2, rms=4.11 012: dt: 0.5000, sse=3125566.0, rms=2.62 013: dt: 0.5000, sse=3648381.5, rms=2.45 rms = 2.41, time step reduction 1 of 3 to 0.250... 014: dt: 0.5000, sse=3838634.0, rms=2.41 015: dt: 0.2500, sse=2731054.0, rms=1.36 016: dt: 0.2500, sse=2569123.0, rms=1.12 rms = 1.08, time step reduction 2 of 3 to 0.125... 017: dt: 0.2500, sse=2483101.0, rms=1.08 rms = 1.04, time step reduction 3 of 3 to 0.062... 018: dt: 0.1250, sse=2446113.5, rms=1.04 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 10 points - only 0.00% unknown deleting segment 1 with 93 points - only 0.00% unknown deleting segment 2 with 48 points - only 0.00% unknown deleting segment 3 with 14 points - only 0.00% unknown deleting segment 4 with 14 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 8 points - only 0.00% unknown deleting segment 8 with 28 points - only 0.00% unknown deleting segment 9 with 10 mean absolute distance = 0.48 +- 0.84 4980 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... points - only 0.00% unknown deleting segment 10 with 636 points - only 0.00% unknown deleting segment 11 with 7 points - only 0.00% unknown deleting segment 12 with 6 points - only 0.00% unknown deleting segment 13 with 6 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 15 with 3 points - only 0.00% unknown deleting segment 16 with 71 points - only 0.00% unknown mean border=84.5, 28 (2) missing vertices, mean dist -0.2 [0.6 (%52.8)->0.3 (%47.2))] %85 local maxima, % 9 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 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 = 0.250 vertex spacing 0.88 +- 0.23 (0.11-->3.09) (max @ vno 62918 --> 61842) face area 0.33 +- 0.14 (0.00-->2.12) 000: dt: 0.0000, sse=2573379.2, rms=2.55 019: dt: 0.5000, sse=2849530.0, rms=1.91 rms = 2.06, time step reduction 1 of 3 to 0.250... 020: dt: 0.2500, sse=2652242.5, rms=1.41 021: dt: 0.2500, sse=2628226.5, rms=1.14 022: dt: 0.2500, sse=2591597.2, rms=1.06 rms = 1.03, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=2581133.5, rms=1.03 rms = 1.01, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=2560513.5, rms=1.01 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 108 points - only 0.00% unknown deleting segment 1 with 49 points - only 0.00% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 16 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 26 points - only 0.00% unknown deleting segment 8 with 11 points - only 0.00% unknown deleting segment 9 with 656 points - only 0.00% unknown deleting smean absolute distance = 0.44 +- 0.74 4520 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... egment 10 with 7 points - only 0.00% unknown deleting segment 11 with 6 points - only 0.00% unknown deleting segment 12 with 8 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 2 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 75 points - only 0.00% unknown mean border=84.7, 25 (0) missing vertices, mean dist -0.1 [0.5 (%48.2)->0.3 (%51.8))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 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 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=2627368.8, rms=1.91 025: dt: 0.5000, sse=3297249.0, rms=1.37 rms = 1.73, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3005548.8, rms=1.02 027: dt: 0.2500, sse=2900170.2, rms=0.91 rms = 0.86, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=2932631.5, rms=0.86 rms = 0.85, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=2927083.5, rms=0.85 positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 2 with 28 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=59.1, 13 (13) missing vertices, mean dist 2.0 [2.4 (%0.0)->2.3 (%100.0))] %18 local maxima, %63 large gradients and %14 min vals, 1721 gradients ignored tol=1.0e-04, sigma=2.0, host=compu, 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 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 30 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=19869610.0, rms=26.70 001: dt: 0.5000, sse=15137655.0, rms=22.99 002: dt: 0.5000, sse=11631006.0, rms=19.79 003: dt: 0.5000, sse=9276887.0, rms=17.12 004: dt: 0.5000, sse=7923744.5, rms=14.81 005: dt: 0.5000, sse=6946663.0, rms=12.84 006: dt: 0.5000, sse=6186188.5, rms=11.17 007: dt: 0.5000, sse=5636904.5, rms=9.75 008: dt: 0.5000, sse=5223909.5, rms=8.51 009: dt: 0.5000, sse=4911481.0, rms=7.44 010: dt: 0.5000, sse=4676241.5, rms=6.49 011: dt: 0.5000, sse=4504130.5, rms=5.67 012: dt: 0.5000, sse=4387223.0, rms=4.94 013: dt: 0.5000, sse=4298063.5, rms=4.32 014: dt: 0.5000, sse=4222284.5, rms=3.79 015: dt: 0.5000, sse=4207833.5, rms=3.37 016: dt: 0.5000, sse=4144591.8, rms=3.02 017: dt: 0.5000, sse=4134545.8, rms=2.78 018: dt: 0.5000, sse=4110298.5, rms=2.57 019: dt: 0.5000, sse=4115040.2, rms=2.44 020: dt: 0.5000, sse=4097396.5, rms=2.33 021: dt: 0.5000, sse=4098103.2, rms=2.27 022: dt: 0.5000, sse=4090320.5, rms=2.20 rms = 2.18, time step reduction 1 of 3 to 0.250... 023: dt: 0.5000, ssesmoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... =4093696.5, rms=2.18 024: dt: 0.2500, sse=2932794.0, rms=1.79 025: dt: 0.2500, sse=2832347.0, rms=1.72 rms = 1.71, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=2797481.8, rms=1.71 rms = 1.69, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=2756895.8, rms=1.69 positioning took 2.6 minutes mean border=56.0, 383 (1) missing vertices, mean dist 0.4 [0.3 (%37.1)->0.8 (%62.9))] %31 local maxima, %53 large gradients and %10 min vals, 1125 gradients ignored tol=1.0e-04, sigma=1.0, host=compu, 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 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 30 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 = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3592617.2, rms=5.10 028: dt: 0.5000, sse=3630096.8, rms=3.73 029: dt: 0.5000, sse=4018470.2, rms=2.94 030: dt: 0.5000, sse=4243187.5, rms=2.55 031: dt: 0.5000, sse=4347688.5, rms=2.33 032: dt: 0.5000, sse=4433499.0, rms=2.22 033: dt: 0.5000, sse=4476095.5, rms=2.17 rms = 2.14, time step reduction 1 of 3 to 0.250... 034: dt: 0.5000, sse=4520546.0, rms=2.14 035: dt: 0.2500, sse=3522783.8, rms=1.77 036: dt: 0.2500, sse=3415526.0, rms=1.70 rms = 1.69, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=3376766.8, rms=1.69 rms = 1.68, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3329131.2, rms=1.68 positioning took 1.0 minutes mean border=55.0, 796 (0) missing vertices, mean dist 0.2 [0.3 (%55.5)->0.8 (%44.5))] %46 local maxima, %38 large gradients and %10 min vals, 682 gradients ignored tol=1.0e-04, sigma=0.5, host=compu, 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 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 30 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 = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3487346.5, rms=2.68 039: dt: 0.5000, sse=3730058.0, rms=2.02 040: dt: 0.5000, sse=4145768.2, rms=1.85 rms = 1.87, time step reduction 1 of 3 to 0.250... 041: dt: 0.2500, sse=3728551.0, rms=1.66 042: dt: 0.2500, sse=3557976.2, rms=1.57 rms = 1.55, time step reduction 2 of 3 to 0.125... 043: dt: 0.2500, sse=3517215.8, rms=1.55 rms = 1.54, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=3470646.2, rms=1.54 positioning took 0.6 minutes mean border=54.2, 1414 (0) missing vertices, mean dist 0.1 [0.3 (%51.3)->0.7 (%48.7))] %60 local maxima, %25 large gradients and %10 min vals, 751 gradients ignored tol=1.0e-04, sigma=0.2, host=compu, 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 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 30 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 writing pial surface to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3541006.0, rms=2.21 045: dt: 0.5000, sse=3771479.8, rms=1.76 046: dt: 0.5000, sse=4044486.2, rms=1.63 rms = 1.72, time step reduction 1 of 3 to 0.250... 047: dt: 0.2500, sse=3740766.5, rms=1.47 048: dt: 0.2500, sse=3624535.5, rms=1.42 rms = 1.41, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=3589499.2, rms=1.41 rms = 1.40, time step reduction 3 of 3 to 0.062... 050: dt: 0.1250, sse=3549114.2, rms=1.40 positioning took 0.6 minutes writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.area.pial vertex spacing 1.04 +- 0.43 (0.07-->8.98) (max @ vno 84580 --> 83514) face area 0.44 +- 0.31 (0.00-->9.06) measuring cortical thickness... 0 of 133655 vertices processed 25000 of 133655 vertices processed 50000 of 133655 vertices processed 75000 of 133655 vertices processed 100000 of 133655 vertices processed 125000 of 133655 vertices processed 0 of 133655 vertices processed 25000 of 133655 vertices processed 50000 of 133655 vertices processed 75000 of 133655 vertices processed 100000 of 133655 vertices processed 125000 of 133655 vertices processed thickness calculation complete, 3488:7460 truncations. 67063 vertices at 0 distance 72741 vertices at 1 distance 58288 vertices at 2 distance 30799 vertices at 3 distance 14319 vertices at 4 distance 5900 vertices at 5 distance 2407 vertices at 6 distance 993 vertices at 7 distance 481 vertices at 8 distance 267 vertices at 9 distance 188 vertices at 10 distance 112 vertices at 11 distance 88 vertices at 12 distance 68 vertices at 13 distance 61 vertices at 14 distance 49 vertices at 15 distance 37 vertices at 16 distance 45 vertices at 17 distance 26 vertices at 18 distance 39 vertices at 19 distancewriting cortical thickness estimate to 'thickness' file. 43 vertices at 20 distance writing curvature file /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.thickness positioning took 11.0 minutes #-------------------------------------------- #@# Surf Volume rh Sat Mar 31 05:28:56 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Sat Mar 31 05:28:57 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts pctsurfcon --s cvs_avg35_inMNI152 --rh-only Log file is /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts/pctsurfcon.log Sat Mar 31 05:28:57 EDT 2012 setenv SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts /usr/local/freesurfer/dev/bin/pctsurfcon $Id: pctsurfcon,v 1.13 2011/11/10 20:21:13 nicks Exp $ Linux compute-0-104.local 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.wm.mgh --regheader cvs_avg35_inMNI152 --cortex srcvol = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz as target reference. Loading label /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label Reading surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 78295 Masking with /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.wm.mgh Dim: 133655 1 1 mri_vol2surf --mov /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.gm.mgh --projfrac 0.3 --regheader cvs_avg35_inMNI152 --cortex srcvol = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/orig.mgz as target reference. Loading label /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label Reading surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Done reading source surface Reading thickness /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 89391 Masking with /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.cortex.label Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.gm.mgh Dim: 133655 1 1 mri_concat /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.wm.mgh /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/tmp.pctsurfcon.14071/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.w-g.pct.mgh --annot cvs_avg35_inMNI152 rh aparc --sum /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.w-g.pct.mgh --annot cvs_avg35_inMNI152 rh aparc --sum /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/stats/rh.w-g.pct.stats --snr sysname Linux hostname compute-0-104.local machine x86_64 user lzollei 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.w-g.pct.mgh Vertex Area is 0.656629 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 9556 6292.16 1 2001 bankssts 1227 833.129 2 2002 caudalanteriorcingulate 1060 655.791 3 2003 caudalmiddlefrontal 3140 2077.16 4 2004 corpuscallosum 0 5 2005 cuneus 2187 1473.94 6 2006 entorhinal 534 360.827 7 2007 fusiform 4751 3116.79 8 2008 inferiorparietal 8122 5325.49 9 2009 inferiortemporal 4575 2995.91 10 2010 isthmuscingulate 1416 915.356 11 2011 lateraloccipital 7706 5105.3 12 2012 lateralorbitofrontal 3198 2093.67 13 2013 lingual 4305 2876.84 14 2014 medialorbitofrontal 2359 1561.27 15 2015 middletemporal 4956 3226 16 2016 parahippocampal 1166 755.458 17 2017 paracentral 2506 1734.65 18 2018 parsopercularis 1939 1221.42 19 2019 parsorbitalis 1131 723.548 20 2020 parstriangularis 2083 1281.46 21 2021 pericalcarine 2132 1402.48 22 2022 postcentral 6177 4198.49 23 2023 posteriorcingulate 1513 1049.5 24 2024 precentral 8040 5268.58 25 2025 precuneus 5638 3671.86 26 2026 rostralanteriorcingulate 862 550.802 27 2027 rostralmiddlefrontal 8003 5099.32 28 2028 superiorfrontal 10087 6582.65 29 2029 superiorparietal 8825 5743.68 30 2030 superiortemporal 5346 3529.05 31 2031 supramarginal 4538 3016.29 32 2032 frontalpole 341 216.585 33 2033 temporalpole 614 377.964 34 2034 transversetemporal 555 351.809 35 2035 insula 3067 2075.31 Reporting on 35 segmentations Cleaning up #----------------------------------------- #@# Parcellation Stats rh Sat Mar 31 05:29:05 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 cvs_avg35_inMNI152 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 1227 833 1717 1.915 0.733 0.093 0.018 6 0.8 bankssts 1060 656 1759 2.293 0.768 0.129 0.045 13 2.3 caudalanteriorcingulate 3140 2077 6364 2.561 0.874 0.123 0.039 28 5.2 caudalmiddlefrontal 2187 1474 4830 2.933 0.907 0.139 0.044 26 4.3 cuneus 534 361 1752 3.258 1.098 0.115 0.027 4 0.6 entorhinal 4751 3117 10160 2.670 1.054 0.127 0.037 52 7.3 fusiform 8122 5325 16963 2.586 0.993 0.126 0.043 92 14.5 inferiorparietal 4575 2996 11439 2.799 1.255 0.125 0.040 48 7.8 inferiortemporal 1416 915 2759 2.717 0.972 0.119 0.035 14 1.9 isthmuscingulate 7706 5105 15941 2.864 0.779 0.139 0.045 90 14.5 lateraloccipital 3198 2094 8441 3.026 1.153 0.118 0.031 30 4.1 lateralorbitofrontal 4305 2877 7988 2.615 0.763 0.146 0.087 99 20.4 lingual 2359 1561 5356 2.498 1.043 0.120 0.041 34 4.1 medialorbitofrontal 4956 3226 12655 2.895 1.160 0.127 0.043 60 8.9 middletemporal 1166 755 1675 1.869 0.929 0.092 0.019 6 0.9 parahippocampal 2506 1735 4452 2.345 0.918 0.103 0.024 14 2.6 paracentral 1939 1221 4123 2.632 0.931 0.115 0.034 18 2.8 parsopercularis 1131 724 3238 3.224 1.008 0.146 0.053 18 2.6 parsorbitalis 2083 1281 4509 2.591 1.090 0.127 0.049 24 4.2 parstriangularis 2132 1402 3172 2.445 0.784 0.133 0.050 41 4.3 pericalcarine 6177 4198 8799 1.811 0.842 0.104 0.025 44 6.4 postcentral 1513 1050 3105 2.419 0.934 0.133 0.041 20 2.4 posteriorcingulate 8040 5269 13314 2.233 0.834 0.110 0.032 61 11.3 precentral 5638 3672 10649 2.490 0.944 0.118 0.037 54 8.6 precuneus 862 551 1708 2.421 0.941 0.107 0.031 6 1.1 rostralanteriorcingulate 8003 5099 18348 2.743 1.025 0.135 0.052 100 17.3 rostralmiddlefrontal 10087 6583 24300 2.803 1.072 0.121 0.042 101 16.9 superiorfrontal 8825 5744 16233 2.354 0.818 0.124 0.040 83 15.2 superiorparietal 5346 3529 12535 2.820 1.080 0.100 0.025 34 5.7 superiortemporal 4538 3016 8733 2.290 1.031 0.117 0.037 45 6.7 supramarginal 341 217 1324 3.716 0.942 0.188 0.090 8 1.3 frontalpole 614 378 2609 3.938 0.838 0.103 0.038 5 0.9 temporalpole 555 352 1109 2.745 0.758 0.127 0.032 5 0.7 transversetemporal 3067 2075 6798 2.898 1.234 0.098 0.051 184 3.5 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat Mar 31 05:29:21 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 cvs_avg35_inMNI152 rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/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 1.721 2012/03/08 13:49:42 fischl Exp $ reading atlas from /usr/local/freesurfer/dev/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... 27 labels changed using aseg relabeling using gibbs priors... 000: 8718 changed, 133655 examined... 001: 1972 changed, 33576 examined... 002: 565 changed, 10252 examined... 003: 211 changed, 3158 examined... 004: 87 changed, 1234 examined... 005: 53 changed, 484 examined... 006: 24 changed, 282 examined... 007: 8 changed, 115 examined... 008: 5 changed, 47 examined... 009: 2 changed, 32 examined... 010: 0 changed, 14 examined... 25 labels changed using aseg 000: 254 total segments, 171 labels (1719 vertices) changed 001: 89 total segments, 7 labels (24 vertices) changed 002: 82 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 146 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 490 vertices marked for relabeling... 490 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 55 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat Mar 31 05:30:16 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 cvs_avg35_inMNI152 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 874 558 2267 2.938 1.095 0.160 0.062 16 2.0 G_and_S_frontomargin 1290 852 3250 3.310 0.712 0.150 0.052 19 2.6 G_and_S_occipital_inf 1488 1034 2682 2.250 0.794 0.117 0.029 11 1.8 G_and_S_paracentral 1308 860 2608 2.277 0.918 0.142 0.045 18 2.4 G_and_S_subcentral 776 487 2819 3.666 0.942 0.144 0.058 10 1.9 G_and_S_transv_frontopol 2601 1664 4919 2.390 0.997 0.105 0.038 24 4.0 G_and_S_cingul-Ant 1337 832 2493 2.319 0.904 0.131 0.053 19 3.4 G_and_S_cingul-Mid-Ant 1284 867 2486 2.304 0.989 0.106 0.031 12 1.4 G_and_S_cingul-Mid-Post 473 319 1514 3.482 0.552 0.181 0.078 10 1.6 G_cingul-Post-dorsal 268 166 788 3.310 1.002 0.137 0.045 3 0.5 G_cingul-Post-ventral 2014 1336 4357 2.823 0.951 0.142 0.045 27 4.0 G_cuneus 1158 727 3008 2.860 0.875 0.124 0.038 13 1.9 G_front_inf-Opercular 232 152 633 2.977 0.790 0.175 0.096 6 1.0 G_front_inf-Orbital 1089 647 3292 3.263 0.961 0.145 0.063 16 2.8 G_front_inf-Triangul 4282 2681 13024 3.275 0.850 0.145 0.060 65 10.8 G_front_middle 6874 4513 19824 3.181 0.958 0.130 0.045 73 12.4 G_front_sup 398 289 1461 3.914 1.115 0.147 0.188 167 0.9 G_Ins_lg_and_S_cent_ins 633 392 2205 3.842 0.995 0.123 0.073 9 1.3 G_insular_short 2549 1629 7821 3.401 0.810 0.148 0.053 39 5.6 G_occipital_middle 2146 1442 4491 2.606 0.828 0.132 0.041 21 3.9 G_occipital_sup 2323 1473 5494 2.994 0.891 0.136 0.042 30 4.1 G_oc-temp_lat-fusifor 2573 1690 5581 2.773 0.686 0.144 0.049 34 5.0 G_oc-temp_med-Lingual 1373 911 3546 2.841 1.142 0.112 0.027 10 1.5 G_oc-temp_med-Parahip 2524 1597 8718 3.630 0.821 0.144 0.049 39 5.3 G_orbital 3072 1941 8316 3.067 0.906 0.146 0.054 48 7.0 G_pariet_inf-Angular 2097 1406 5835 2.898 1.027 0.130 0.046 25 3.9 G_pariet_inf-Supramar 2515 1639 5943 2.752 0.726 0.131 0.040 27 4.5 G_parietal_sup 2324 1574 3933 2.071 0.847 0.113 0.026 19 2.5 G_postcentral 3030 2011 6611 2.596 0.761 0.114 0.031 22 3.9 G_precentral 2677 1746 6618 2.872 0.801 0.142 0.048 36 5.5 G_precuneus 713 494 2204 2.829 0.920 0.152 0.061 18 2.0 G_rectus 77 62 176 3.005 0.305 0.067 0.024 0 0.0 G_subcallosal 435 272 1030 3.139 0.613 0.127 0.034 4 0.5 G_temp_sup-G_T_transv 1728 1164 5886 3.442 0.883 0.133 0.036 18 2.7 G_temp_sup-Lateral 647 439 1688 3.136 0.812 0.064 0.011 1 0.3 G_temp_sup-Plan_polar 719 486 1779 2.884 1.031 0.110 0.031 7 1.0 G_temp_sup-Plan_tempo 2279 1512 7502 3.327 1.076 0.137 0.047 28 4.6 G_temporal_inf 2927 1875 9727 3.379 1.068 0.149 0.058 49 7.0 G_temporal_middle 311 201 301 1.542 0.525 0.089 0.016 2 0.2 Lat_Fis-ant-Horizont 238 140 555 3.044 0.864 0.144 0.084 4 0.9 Lat_Fis-ant-Vertical 1522 1015 1809 1.805 0.683 0.090 0.016 6 1.0 Lat_Fis-post 3259 2215 6226 2.584 0.710 0.143 0.045 39 6.3 Pole_occipital 1761 1135 6889 3.640 1.177 0.143 0.052 27 3.9 Pole_temporal 2312 1568 3322 2.432 0.855 0.130 0.111 75 15.3 S_calcarine 3338 2257 3195 1.529 0.560 0.089 0.021 15 3.1 S_central 1318 898 1615 1.726 0.600 0.097 0.022 7 1.1 S_cingul-Marginalis 536 365 940 2.682 0.907 0.105 0.025 3 0.5 S_circular_insula_ant 1452 926 1782 2.068 0.988 0.063 0.010 3 0.7 S_circular_insula_inf 1405 948 1597 1.847 0.529 0.085 0.018 5 1.1 S_circular_insula_sup 773 522 900 1.653 0.517 0.084 0.014 3 0.5 S_collat_transv_ant 604 396 877 2.848 0.738 0.128 0.041 6 0.9 S_collat_transv_post 2221 1463 3278 2.169 0.691 0.121 0.037 20 3.6 S_front_inf 1735 1136 2531 2.201 0.720 0.110 0.035 10 2.4 S_front_middle 2479 1671 3197 1.912 0.619 0.111 0.030 16 3.3 S_front_sup 390 250 302 1.498 0.452 0.133 0.043 6 0.8 S_interm_prim-Jensen 3587 2305 4827 2.085 0.660 0.119 0.045 33 6.7 S_intrapariet_and_P_trans 1513 1015 2612 2.655 0.739 0.127 0.039 11 2.6 S_oc_middle_and_Lunatus 1378 905 1469 1.821 0.490 0.116 0.035 10 2.0 S_oc_sup_and_transversal 1081 716 2002 2.989 0.884 0.121 0.039 10 1.5 S_occipital_ant 1047 674 1161 1.843 0.621 0.104 0.031 6 1.3 S_oc-temp_lat 2041 1349 2405 1.889 0.839 0.109 0.034 24 3.2 S_oc-temp_med_and_Lingual 451 301 684 1.920 0.649 0.124 0.048 4 0.7 S_orbital_lateral 640 431 1097 2.219 0.716 0.095 0.015 3 0.3 S_orbital_med-olfact 1255 831 2358 2.451 1.211 0.092 0.020 6 1.1 S_orbital-H_Shaped 2183 1428 3219 2.358 0.770 0.106 0.031 14 2.9 S_parieto_occipital 1639 1041 1786 2.133 0.670 0.112 0.024 16 1.4 S_pericallosal 2444 1643 2303 1.522 0.549 0.089 0.021 13 2.0 S_postcentral 1645 1060 2505 2.268 0.873 0.111 0.036 15 2.8 S_precentral-inf-part 1551 1017 1964 2.028 0.811 0.111 0.033 13 2.2 S_precentral-sup-part 249 174 490 2.548 1.273 0.096 0.011 1 0.1 S_suborbital 1168 730 1899 2.227 1.013 0.115 0.038 12 1.7 S_subparietal 1323 877 1705 2.160 0.970 0.113 0.028 8 1.8 S_temporal_inf 5844 3920 7962 2.017 0.745 0.089 0.020 29 4.6 S_temporal_sup 299 208 563 3.024 0.952 0.109 0.021 2 0.3 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Sat Mar 31 05:30:33 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon cvs_avg35_inMNI152 SUBJECTS_DIR is /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI 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 = 12 writing volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat Mar 31 05:41:25 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject cvs_avg35_inMNI152 $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject cvs_avg35_inMNI152 sysname Linux hostname compute-0-104.local machine x86_64 user lzollei atlas_icv (eTIV) = 1536505 mm^3 (det: 1.267881 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 315352 rh white matter volume 315562 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 349226.998223, pTot = 610355.919294 c = 261128.921072 rh surface-based volumes (mm3): wTot = 347569.591927, pTot = 604422.091870 c = 256852.499944 Computing SupraTentVolCor SupraTentVolCor = 7541.000 SupraTentVol = 1222319.011 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 7616 7616 4 5 Left-Inf-Lat-Vent 94 94 5 7 Left-Cerebellum-White-Matter 19775 19775 6 8 Left-Cerebellum-Cortex 64792 64792 7 10 Left-Thalamus-Proper 10390 10390 8 11 Left-Caudate 4632 4632 9 12 Left-Putamen 8067 8067 10 13 Left-Pallidum 2239 2239 11 14 3rd-Ventricle 956 956 12 15 4th-Ventricle 1810 1810 13 16 Brain-Stem 28764 28764 14 17 Left-Hippocampus 5730 5730 15 18 Left-Amygdala 1797 1797 16 24 CSF 1296 1296 17 26 Left-Accumbens-area 837 837 18 28 Left-VentralDC 5516 5516 19 30 Left-vessel 57 57 20 31 Left-choroid-plexus 2520 2520 23 43 Right-Lateral-Ventricle 6500 6500 24 44 Right-Inf-Lat-Vent 360 360 25 46 Right-Cerebellum-White-Matter 19526 19526 26 47 Right-Cerebellum-Cortex 68252 68252 27 49 Right-Thalamus-Proper 10601 10601 28 50 Right-Caudate 4803 4803 29 51 Right-Putamen 7882 7882 30 52 Right-Pallidum 2303 2303 31 53 Right-Hippocampus 5454 5454 32 54 Right-Amygdala 1958 1958 33 58 Right-Accumbens-area 1068 1068 34 60 Right-VentralDC 5353 5353 35 62 Right-vessel 39 39 36 63 Right-choroid-plexus 2637 2637 37 72 5th-Ventricle 0 38 77 WM-hypointensities 6958 6958 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 67 67 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 343 343 45 251 CC_Posterior 1085 1085 46 252 CC_Mid_Posterior 431 431 47 253 CC_Central 475 475 48 254 CC_Mid_Anterior 483 483 49 255 CC_Anterior 973 973 Reporting on 45 segmentations SubCortGrayVol = 240438 #----------------------------------------- #@# AParc-to-ASeg Sat Mar 31 05:52:35 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_aparc2aseg --s cvs_avg35_inMNI152 --volmask SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI subject cvs_avg35_inMNI152 outvol /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading lh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial Loading lh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading rh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial Loading rh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 508742 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aparc+aseg.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_aparc2aseg --s cvs_avg35_inMNI152 --volmask --a2009s SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI subject cvs_avg35_inMNI152 outvol /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading lh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial Loading lh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading rh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial Loading rh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 508742 Used brute-force search on 0 voxels Writing output aseg to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Sat Mar 31 05:55:13 EDT 2012 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_aparc2aseg --s cvs_avg35_inMNI152 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI subject cvs_avg35_inMNI152 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aparc+aseg.mgz Reading lh white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading lh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial Loading lh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading rh pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial Loading rh annotations from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/ribbon.mgz Loading filled from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/filled.mgz Ripping vertices labeled as unkown Ripped 9012 vertices from left hemi Ripped 9556 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/aseg.mgz Loading Ctx Seg File /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 = 1116783 Used brute-force search on 1334 voxels Fixing Parahip LH WM Found 8 clusters 0 k 1.000000 1 k 1767.000000 2 k 1.000000 3 k 1.000000 4 k 1.000000 5 k 1.000000 6 k 2.000000 7 k 3.000000 Fixing Parahip RH WM Found 8 clusters 0 k 1.000000 1 k 1877.000000 2 k 8.000000 3 k 1.000000 4 k 1.000000 5 k 2.000000 6 k 1.000000 7 k 2.000000 Writing output aseg to mri/wmparc.mgz /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152 mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject cvs_avg35_inMNI152 --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.81 2012/01/20 22:17:36 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject cvs_avg35_inMNI152 --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv sysname Linux hostname compute-0-104.local machine x86_64 user lzollei atlas_icv (eTIV) = 1536505 mm^3 (det: 1.267881 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 315352 rh white matter volume 315562 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1962261 # brainmaskvolume 1962261.0 # nbrainsegvoxels 303549 # brainsegvolume 303549.0 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 1 3001 wm-lh-bankssts 3894 3894 2 3002 wm-lh-caudalanteriorcingulate 2940 2940 3 3003 wm-lh-caudalmiddlefrontal 8690 8690 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 3316 3316 6 3006 wm-lh-entorhinal 935 935 7 3007 wm-lh-fusiform 8103 8103 8 3008 wm-lh-inferiorparietal 11855 11855 9 3009 wm-lh-inferiortemporal 8497 8497 10 3010 wm-lh-isthmuscingulate 4169 4169 11 3011 wm-lh-lateraloccipital 13984 13984 12 3012 wm-lh-lateralorbitofrontal 7326 7326 13 3013 wm-lh-lingual 5736 5736 14 3014 wm-lh-medialorbitofrontal 4325 4325 15 3015 wm-lh-middletemporal 6472 6472 16 3016 wm-lh-parahippocampal 1951 1951 17 3017 wm-lh-paracentral 4758 4758 18 3018 wm-lh-parsopercularis 4495 4495 19 3019 wm-lh-parsorbitalis 857 857 20 3020 wm-lh-parstriangularis 3274 3274 21 3021 wm-lh-pericalcarine 4432 4432 22 3022 wm-lh-postcentral 10440 10440 23 3023 wm-lh-posteriorcingulate 5117 5117 24 3024 wm-lh-precentral 18761 18761 25 3025 wm-lh-precuneus 11183 11183 26 3026 wm-lh-rostralanteriorcingulate 3085 3085 27 3027 wm-lh-rostralmiddlefrontal 14753 14753 28 3028 wm-lh-superiorfrontal 22628 22628 29 3029 wm-lh-superiorparietal 17315 17315 30 3030 wm-lh-superiortemporal 9413 9413 31 3031 wm-lh-supramarginal 11356 11356 32 3032 wm-lh-frontalpole 219 219 33 3033 wm-lh-temporalpole 790 790 34 3034 wm-lh-transversetemporal 888 888 35 3035 wm-lh-insula 9110 9110 36 3100 wm-lh-Unknown 0 37 3101 wm-lh-Corpus_callosum 0 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 39 3103 wm-lh-G_cingulate-Isthmus 0 40 3104 wm-lh-G_cingulate-Main_part 0 41 3105 wm-lh-G_cuneus 0 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 45 3109 wm-lh-G_frontal_middle 0 46 3110 wm-lh-G_frontal_superior 0 47 3111 wm-lh-G_frontomarginal 0 48 3112 wm-lh-G_insular_long 0 49 3113 wm-lh-G_insular_short 0 50 3114 wm-lh-G_and_S_occipital_inferior 0 51 3115 wm-lh-G_occipital_middle 0 52 3116 wm-lh-G_occipital_superior 0 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 56 3120 wm-lh-G_orbital 0 57 3121 wm-lh-G_paracentral 0 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 60 3124 wm-lh-G_parietal_superior 0 61 3125 wm-lh-G_postcentral 0 62 3126 wm-lh-G_precentral 0 63 3127 wm-lh-G_precuneus 0 64 3128 wm-lh-G_rectus 0 65 3129 wm-lh-G_subcallosal 0 66 3130 wm-lh-G_subcentral 0 67 3131 wm-lh-G_temporal_inferior 0 68 3132 wm-lh-G_temporal_middle 0 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 71 3135 wm-lh-G_temp_sup-Planum_polare 0 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 76 3140 wm-lh-Lat_Fissure-post_sgt 0 77 3141 wm-lh-Medial_wall 0 78 3142 wm-lh-Pole_occipital 0 79 3143 wm-lh-Pole_temporal 0 80 3144 wm-lh-S_calcarine 0 81 3145 wm-lh-S_central 0 82 3146 wm-lh-S_central_insula 0 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 84 3148 wm-lh-S_cingulate-Marginalis_part 0 85 3149 wm-lh-S_circular_insula_anterior 0 86 3150 wm-lh-S_circular_insula_inferior 0 87 3151 wm-lh-S_circular_insula_superior 0 88 3152 wm-lh-S_collateral_transverse_ant 0 89 3153 wm-lh-S_collateral_transverse_post 0 90 3154 wm-lh-S_frontal_inferior 0 91 3155 wm-lh-S_frontal_middle 0 92 3156 wm-lh-S_frontal_superior 0 93 3157 wm-lh-S_frontomarginal 0 94 3158 wm-lh-S_intermedius_primus-Jensen 0 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 96 3160 wm-lh-S_occipital_anterior 0 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 99 3163 wm-lh-S_occipito-temporal_lateral 0 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 101 3165 wm-lh-S_orbital-H_shapped 0 102 3166 wm-lh-S_orbital_lateral 0 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 104 3168 wm-lh-S_paracentral 0 105 3169 wm-lh-S_parieto_occipital 0 106 3170 wm-lh-S_pericallosal 0 107 3171 wm-lh-S_postcentral 0 108 3172 wm-lh-S_precentral-Inferior-part 0 109 3173 wm-lh-S_precentral-Superior-part 0 110 3174 wm-lh-S_subcentral_ant 0 111 3175 wm-lh-S_subcentral_post 0 112 3176 wm-lh-S_suborbital 0 113 3177 wm-lh-S_subparietal 0 114 3178 wm-lh-S_supracingulate 0 115 3179 wm-lh-S_temporal_inferior 0 116 3180 wm-lh-S_temporal_superior 0 117 3181 wm-lh-S_temporal_transverse 0 118 4000 wm-rh-unknown 0 119 4001 wm-rh-bankssts 2754 2754 120 4002 wm-rh-caudalanteriorcingulate 3201 3201 121 4003 wm-rh-caudalmiddlefrontal 6987 6987 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 3517 3517 124 4006 wm-rh-entorhinal 908 908 125 4007 wm-rh-fusiform 7877 7877 126 4008 wm-rh-inferiorparietal 14330 14330 127 4009 wm-rh-inferiortemporal 7916 7916 128 4010 wm-rh-isthmuscingulate 3865 3865 129 4011 wm-rh-lateraloccipital 14348 14348 130 4012 wm-rh-lateralorbitofrontal 7073 7073 131 4013 wm-rh-lingual 7327 7327 132 4014 wm-rh-medialorbitofrontal 3651 3651 133 4015 wm-rh-middletemporal 7511 7511 134 4016 wm-rh-parahippocampal 2061 2061 135 4017 wm-rh-paracentral 6441 6441 136 4018 wm-rh-parsopercularis 3930 3930 137 4019 wm-rh-parsorbitalis 1388 1388 138 4020 wm-rh-parstriangularis 3750 3750 139 4021 wm-rh-pericalcarine 4756 4756 140 4022 wm-rh-postcentral 9103 9103 141 4023 wm-rh-posteriorcingulate 4565 4565 142 4024 wm-rh-precentral 18110 18110 143 4025 wm-rh-precuneus 11852 11852 144 4026 wm-rh-rostralanteriorcingulate 2439 2439 145 4027 wm-rh-rostralmiddlefrontal 15166 15166 146 4028 wm-rh-superiorfrontal 22506 22506 147 4029 wm-rh-superiorparietal 16506 16506 148 4030 wm-rh-superiortemporal 7590 7590 149 4031 wm-rh-supramarginal 8499 8499 150 4032 wm-rh-frontalpole 347 347 151 4033 wm-rh-temporalpole 847 847 152 4034 wm-rh-transversetemporal 787 787 153 4035 wm-rh-insula 8959 8959 154 4100 wm-rh-Unknown 0 155 4101 wm-rh-Corpus_callosum 0 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 157 4103 wm-rh-G_cingulate-Isthmus 0 158 4104 wm-rh-G_cingulate-Main_part 0 159 4105 wm-rh-G_cuneus 0 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 163 4109 wm-rh-G_frontal_middle 0 164 4110 wm-rh-G_frontal_superior 0 165 4111 wm-rh-G_frontomarginal 0 166 4112 wm-rh-G_insular_long 0 167 4113 wm-rh-G_insular_short 0 168 4114 wm-rh-G_and_S_occipital_inferior 0 169 4115 wm-rh-G_occipital_middle 0 170 4116 wm-rh-G_occipital_superior 0 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 174 4120 wm-rh-G_orbital 0 175 4121 wm-rh-G_paracentral 0 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 178 4124 wm-rh-G_parietal_superior 0 179 4125 wm-rh-G_postcentral 0 180 4126 wm-rh-G_precentral 0 181 4127 wm-rh-G_precuneus 0 182 4128 wm-rh-G_rectus 0 183 4129 wm-rh-G_subcallosal 0 184 4130 wm-rh-G_subcentral 0 185 4131 wm-rh-G_temporal_inferior 0 186 4132 wm-rh-G_temporal_middle 0 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 189 4135 wm-rh-G_temp_sup-Planum_polare 0 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 194 4140 wm-rh-Lat_Fissure-post_sgt 0 195 4141 wm-rh-Medial_wall 0 196 4142 wm-rh-Pole_occipital 0 197 4143 wm-rh-Pole_temporal 0 198 4144 wm-rh-S_calcarine 0 199 4145 wm-rh-S_central 0 200 4146 wm-rh-S_central_insula 0 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 202 4148 wm-rh-S_cingulate-Marginalis_part 0 203 4149 wm-rh-S_circular_insula_anterior 0 204 4150 wm-rh-S_circular_insula_inferior 0 205 4151 wm-rh-S_circular_insula_superior 0 206 4152 wm-rh-S_collateral_transverse_ant 0 207 4153 wm-rh-S_collateral_transverse_post 0 208 4154 wm-rh-S_frontal_inferior 0 209 4155 wm-rh-S_frontal_middle 0 210 4156 wm-rh-S_frontal_superior 0 211 4157 wm-rh-S_frontomarginal 0 212 4158 wm-rh-S_intermedius_primus-Jensen 0 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 214 4160 wm-rh-S_occipital_anterior 0 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 217 4163 wm-rh-S_occipito-temporal_lateral 0 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 219 4165 wm-rh-S_orbital-H_shapped 0 220 4166 wm-rh-S_orbital_lateral 0 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 222 4168 wm-rh-S_paracentral 0 223 4169 wm-rh-S_parieto_occipital 0 224 4170 wm-rh-S_pericallosal 0 225 4171 wm-rh-S_postcentral 0 226 4172 wm-rh-S_precentral-Inferior-part 0 227 4173 wm-rh-S_precentral-Superior-part 0 228 4174 wm-rh-S_subcentral_ant 0 229 4175 wm-rh-S_subcentral_post 0 230 4176 wm-rh-S_suborbital 0 231 4177 wm-rh-S_subparietal 0 232 4178 wm-rh-S_supracingulate 0 233 4179 wm-rh-S_temporal_inferior 0 234 4180 wm-rh-S_temporal_superior 0 235 4181 wm-rh-S_temporal_transverse 0 236 5001 Left-UnsegmentedWhiteMatter 55907 55907 237 5002 Right-UnsegmentedWhiteMatter 57962 57962 238 13100 wm_lh_Unknown 0 239 13101 wm_lh_G_and_S_frontomargin 0 240 13102 wm_lh_G_and_S_occipital_inf 0 241 13103 wm_lh_G_and_S_paracentral 0 242 13104 wm_lh_G_and_S_subcentral 0 243 13105 wm_lh_G_and_S_transv_frontopol 0 244 13106 wm_lh_G_and_S_cingul-Ant 0 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 247 13109 wm_lh_G_cingul-Post-dorsal 0 248 13110 wm_lh_G_cingul-Post-ventral 0 249 13111 wm_lh_G_cuneus 0 250 13112 wm_lh_G_front_inf-Opercular 0 251 13113 wm_lh_G_front_inf-Orbital 0 252 13114 wm_lh_G_front_inf-Triangul 0 253 13115 wm_lh_G_front_middle 0 254 13116 wm_lh_G_front_sup 0 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 256 13118 wm_lh_G_insular_short 0 257 13119 wm_lh_G_occipital_middle 0 258 13120 wm_lh_G_occipital_sup 0 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 260 13122 wm_lh_G_oc-temp_med-Lingual 0 261 13123 wm_lh_G_oc-temp_med-Parahip 0 262 13124 wm_lh_G_orbital 0 263 13125 wm_lh_G_pariet_inf-Angular 0 264 13126 wm_lh_G_pariet_inf-Supramar 0 265 13127 wm_lh_G_parietal_sup 0 266 13128 wm_lh_G_postcentral 0 267 13129 wm_lh_G_precentral 0 268 13130 wm_lh_G_precuneus 0 269 13131 wm_lh_G_rectus 0 270 13132 wm_lh_G_subcallosal 0 271 13133 wm_lh_G_temp_sup-G_T_transv 0 272 13134 wm_lh_G_temp_sup-Lateral 0 273 13135 wm_lh_G_temp_sup-Plan_polar 0 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 275 13137 wm_lh_G_temporal_inf 0 276 13138 wm_lh_G_temporal_middle 0 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 279 13141 wm_lh_Lat_Fis-post 0 280 13142 wm_lh_Medial_wall 0 281 13143 wm_lh_Pole_occipital 0 282 13144 wm_lh_Pole_temporal 0 283 13145 wm_lh_S_calcarine 0 284 13146 wm_lh_S_central 0 285 13147 wm_lh_S_cingul-Marginalis 0 286 13148 wm_lh_S_circular_insula_ant 0 287 13149 wm_lh_S_circular_insula_inf 0 288 13150 wm_lh_S_circular_insula_sup 0 289 13151 wm_lh_S_collat_transv_ant 0 290 13152 wm_lh_S_collat_transv_post 0 291 13153 wm_lh_S_front_inf 0 292 13154 wm_lh_S_front_middle 0 293 13155 wm_lh_S_front_sup 0 294 13156 wm_lh_S_interm_prim-Jensen 0 295 13157 wm_lh_S_intrapariet_and_P_trans 0 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 297 13159 wm_lh_S_oc_sup_and_transversal 0 298 13160 wm_lh_S_occipital_ant 0 299 13161 wm_lh_S_oc-temp_lat 0 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 301 13163 wm_lh_S_orbital_lateral 0 302 13164 wm_lh_S_orbital_med-olfact 0 303 13165 wm_lh_S_orbital-H_Shaped 0 304 13166 wm_lh_S_parieto_occipital 0 305 13167 wm_lh_S_pericallosal 0 306 13168 wm_lh_S_postcentral 0 307 13169 wm_lh_S_precentral-inf-part 0 308 13170 wm_lh_S_precentral-sup-part 0 309 13171 wm_lh_S_suborbital 0 310 13172 wm_lh_S_subparietal 0 311 13173 wm_lh_S_temporal_inf 0 312 13174 wm_lh_S_temporal_sup 0 313 13175 wm_lh_S_temporal_transverse 0 314 14100 wm_rh_Unknown 0 315 14101 wm_rh_G_and_S_frontomargin 0 316 14102 wm_rh_G_and_S_occipital_inf 0 317 14103 wm_rh_G_and_S_paracentral 0 318 14104 wm_rh_G_and_S_subcentral 0 319 14105 wm_rh_G_and_S_transv_frontopol 0 320 14106 wm_rh_G_and_S_cingul-Ant 0 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 323 14109 wm_rh_G_cingul-Post-dorsal 0 324 14110 wm_rh_G_cingul-Post-ventral 0 325 14111 wm_rh_G_cuneus 0 326 14112 wm_rh_G_front_inf-Opercular 0 327 14113 wm_rh_G_front_inf-Orbital 0 328 14114 wm_rh_G_front_inf-Triangul 0 329 14115 wm_rh_G_front_middle 0 330 14116 wm_rh_G_front_sup 0 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 332 14118 wm_rh_G_insular_short 0 333 14119 wm_rh_G_occipital_middle 0 334 14120 wm_rh_G_occipital_sup 0 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 336 14122 wm_rh_G_oc-temp_med-Lingual 0 337 14123 wm_rh_G_oc-temp_med-Parahip 0 338 14124 wm_rh_G_orbital 0 339 14125 wm_rh_G_pariet_inf-Angular 0 340 14126 wm_rh_G_pariet_inf-Supramar 0 341 14127 wm_rh_G_parietal_sup 0 342 14128 wm_rh_G_postcentral 0 343 14129 wm_rh_G_precentral 0 344 14130 wm_rh_G_precuneus 0 345 14131 wm_rh_G_rectus 0 346 14132 wm_rh_G_subcallosal 0 347 14133 wm_rh_G_temp_sup-G_T_transv 0 348 14134 wm_rh_G_temp_sup-Lateral 0 349 14135 wm_rh_G_temp_sup-Plan_polar 0 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 351 14137 wm_rh_G_temporal_inf 0 352 14138 wm_rh_G_temporal_middle 0 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 355 14141 wm_rh_Lat_Fis-post 0 356 14142 wm_rh_Medial_wall 0 357 14143 wm_rh_Pole_occipital 0 358 14144 wm_rh_Pole_temporal 0 359 14145 wm_rh_S_calcarine 0 360 14146 wm_rh_S_central 0 361 14147 wm_rh_S_cingul-Marginalis 0 362 14148 wm_rh_S_circular_insula_ant 0 363 14149 wm_rh_S_circular_insula_inf 0 364 14150 wm_rh_S_circular_insula_sup 0 365 14151 wm_rh_S_collat_transv_ant 0 366 14152 wm_rh_S_collat_transv_post 0 367 14153 wm_rh_S_front_inf 0 368 14154 wm_rh_S_front_middle 0 369 14155 wm_rh_S_front_sup 0 370 14156 wm_rh_S_interm_prim-Jensen 0 371 14157 wm_rh_S_intrapariet_and_P_trans 0 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 373 14159 wm_rh_S_oc_sup_and_transversal 0 374 14160 wm_rh_S_occipital_ant 0 375 14161 wm_rh_S_oc-temp_lat 0 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 377 14163 wm_rh_S_orbital_lateral 0 378 14164 wm_rh_S_orbital_med-olfact 0 379 14165 wm_rh_S_orbital-H_Shaped 0 380 14166 wm_rh_S_parieto_occipital 0 381 14167 wm_rh_S_pericallosal 0 382 14168 wm_rh_S_postcentral 0 383 14169 wm_rh_S_precentral-inf-part 0 384 14170 wm_rh_S_precentral-sup-part 0 385 14171 wm_rh_S_suborbital 0 386 14172 wm_rh_S_subparietal 0 387 14173 wm_rh_S_temporal_inf 0 388 14174 wm_rh_S_temporal_sup 0 389 14175 wm_rh_S_temporal_transverse 0 Reporting on 70 segmentations /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label #-------------------------------------------- #@# BA Labels lh Sat Mar 31 06:16:30 EDT 2012 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI; ln -s /usr/local/freesurfer/dev/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA1.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 432 Checking for and removing duplicates Writing label file ./lh.BA1.label 4561 LabelWrite: saving to ./lh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA2.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 954 Checking for and removing duplicates Writing label file ./lh.BA2.label 8863 LabelWrite: saving to ./lh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA3a.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 238 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4315 LabelWrite: saving to ./lh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA3b.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 499 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6482 LabelWrite: saving to ./lh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA4a.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 428 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6212 LabelWrite: saving to ./lh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA4p.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 296 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4366 LabelWrite: saving to ./lh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA6.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 1582 Checking for and removing duplicates Writing label file ./lh.BA6.label 15171 LabelWrite: saving to ./lh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA44.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 502 Checking for and removing duplicates Writing label file ./lh.BA44.label 4683 LabelWrite: saving to ./lh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA45.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 717 Checking for and removing duplicates Writing label file ./lh.BA45.label 4139 LabelWrite: saving to ./lh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.V1.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 916 Checking for and removing duplicates Writing label file ./lh.V1.label 5557 LabelWrite: saving to ./lh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.V2.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 2304 Checking for and removing duplicates Writing label file ./lh.V2.label 10418 LabelWrite: saving to ./lh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.MT.label --trgsubject cvs_avg35_inMNI152 --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 549 Checking for and removing duplicates Writing label file ./lh.MT.label 2567 LabelWrite: saving to ./lh.MT.label mri_label2label: Done mris_label2annot --s cvs_avg35_inMNI152 --hemi lh --ctab /usr/local/freesurfer/dev/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 --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label cmdline mris_label2annot --s cvs_avg35_inMNI152 --hemi lh --ctab /usr/local/freesurfer/dev/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 --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-104.local machine x86_64 user lzollei subject cvs_avg35_inMNI152 hemi lh SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 95377 unhit vertices Writing annot to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/lh.BA.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab cvs_avg35_inMNI152 lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/dev/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 1094 717 1874 2.114 0.603 0.130 0.040 11 1.8 BA1 4751 3111 6839 2.011 0.900 0.130 0.088 184 15.7 BA2 1155 751 1016 1.733 0.570 0.123 0.038 9 1.8 BA3a 2741 1778 4066 1.903 0.802 0.118 0.033 25 4.1 BA3b 1885 1200 3328 2.360 0.702 0.112 0.031 13 2.6 BA4a 1525 1011 1852 1.864 0.534 0.091 0.023 6 1.5 BA4p 10041 6575 22306 2.785 0.991 0.121 0.038 87 16.3 BA6 2628 1646 5448 2.599 0.867 0.130 0.071 51 7.0 BA44 3019 1911 6844 2.530 1.045 0.134 0.055 42 7.1 BA45 3070 2064 6143 2.700 0.894 0.126 0.226 58 4.9 V1 7902 5122 15717 2.754 0.809 0.145 0.076 132 17.0 V2 2239 1429 4492 2.859 0.972 0.133 0.043 26 4.0 MT #-------------------------------------------- #@# BA Labels rh Sat Mar 31 06:18:45 EDT 2012 mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA1.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 249 Checking for and removing duplicates Writing label file ./rh.BA1.label 4211 LabelWrite: saving to ./rh.BA1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA2.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 342 Checking for and removing duplicates Writing label file ./rh.BA2.label 7029 LabelWrite: saving to ./rh.BA2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA3a.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 204 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4184 LabelWrite: saving to ./rh.BA3a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA3b.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 275 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4797 LabelWrite: saving to ./rh.BA3b.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA4a.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 376 Checking for and removing duplicates Writing label file ./rh.BA4a.label 6123 LabelWrite: saving to ./rh.BA4a.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA4p.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 230 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4703 LabelWrite: saving to ./rh.BA4p.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA6.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 1111 Checking for and removing duplicates Writing label file ./rh.BA6.label 13367 LabelWrite: saving to ./rh.BA6.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA44.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 782 Checking for and removing duplicates Writing label file ./rh.BA44.label 7694 LabelWrite: saving to ./rh.BA44.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA45.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 908 Checking for and removing duplicates Writing label file ./rh.BA45.label 6263 LabelWrite: saving to ./rh.BA45.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.V1.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 1320 Checking for and removing duplicates Writing label file ./rh.V1.label 6047 LabelWrite: saving to ./rh.V1.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.V2.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 2724 Checking for and removing duplicates Writing label file ./rh.V2.label 10740 LabelWrite: saving to ./rh.V2.label mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.MT.label --trgsubject cvs_avg35_inMNI152 --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = cvs_avg35_inMNI152 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 /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white Reading target registration /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 Number of reverse mapping hits = 714 Checking for and removing duplicates Writing label file ./rh.MT.label 2646 LabelWrite: saving to ./rh.MT.label mri_label2label: Done mris_label2annot --s cvs_avg35_inMNI152 --hemi rh --ctab /usr/local/freesurfer/dev/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 --a BA --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 13 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label cmdline mris_label2annot --s cvs_avg35_inMNI152 --hemi rh --ctab /usr/local/freesurfer/dev/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 --a BA --maxstatwinner --noverbose sysname Linux hostname compute-0-104.local machine x86_64 user lzollei subject cvs_avg35_inMNI152 hemi rh SUBJECTS_DIR /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA nlables 12 LabelThresh 0 0.000000 Loading /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 92202 unhit vertices Writing annot to /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label/rh.BA.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab cvs_avg35_inMNI152 rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 13 entries read (originally /usr/local/freesurfer/dev/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 888 595 1619 2.147 0.561 0.140 0.034 10 1.3 BA1 3297 2215 4336 1.857 0.804 0.094 0.021 17 2.9 BA2 1154 749 1021 1.580 0.580 0.119 0.033 9 1.7 BA3a 2112 1452 2561 1.493 0.651 0.091 0.018 11 1.6 BA3b 1612 1128 3124 2.464 0.755 0.098 0.024 7 1.7 BA4a 1373 940 1669 1.760 0.521 0.089 0.020 6 1.2 BA4p 8581 5659 19425 2.738 0.974 0.120 0.036 74 13.0 BA6 3625 2303 6674 2.406 0.927 0.115 0.036 33 5.8 BA44 4228 2647 9996 2.751 1.060 0.133 0.051 55 9.1 BA45 3791 2555 6652 2.406 0.739 0.136 0.079 70 16.5 V1 8345 5575 16414 2.801 0.783 0.142 0.049 127 18.1 V2 2447 1635 5621 3.027 0.894 0.124 0.040 20 4.0 MT /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Sat Mar 31 06:20:56 EDT 2012 INFO: lh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to lh.EC_average subject... cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI; ln -s /usr/local/freesurfer/dev/subjects/lh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o cvs_avg35_inMNI152 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject cvs_avg35_inMNI152. processing subject lh.EC_average... reading output surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 931 points to lh.entorhinal_exvivo.label... LabelWrite: saving to lh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label cvs_avg35_inMNI152 lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/lh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 312 188 1045 3.090 1.139 0.103 0.019 2 0.3 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Sat Mar 31 06:21:15 EDT 2012 INFO: rh.EC_average subject does not exist in SUBJECTS_DIR INFO: Creating symlink to rh.EC_average subject... cd /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI; ln -s /usr/local/freesurfer/dev/subjects/rh.EC_average; cd - mris_spherical_average -erode 1 -orig white -t 0.4 -o cvs_avg35_inMNI152 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject cvs_avg35_inMNI152. processing subject rh.EC_average... reading output surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 774 points to rh.entorhinal_exvivo.label... LabelWrite: saving to rh.entorhinal_exvivo.label mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label cvs_avg35_inMNI152 rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/mri/wm.mgz... reading input surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.white... reading input pial surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/surf/rh.pial... reading input white surface /autofs/space/erdos_003/users/lzollei/my_stuff/research/tests/CVSvsMNI/cvs_avg35_inMNI152/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 274 176 896 3.049 0.898 0.107 0.020 2 0.3 ./rh.entorhinal_exvivo.label #------------------------------------------ recon-all -s cvs_avg35_inMNI152 finished without error at Sat Mar 31 06:21:36 EDT 2012