Wed Aug 17 13:37:50 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 /export/data1/tools/freesurfer/bin/recon-all -s NF108_11 -i /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw/MRDC.00001 -force subjid NF108_11 setenv SUBJECTS_DIR /export/data1/tools/freesurfer/subjects/hannahas FREESURFER_HOME /export/data1/tools/freesurfer Actual FREESURFER_HOME /export/data1/tools/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16466344 13670984 2795360 0 240444 12045880 -/+ buffers/cache: 1384660 15081684 Swap: 18579448 0 18579448 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:37:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /export/data1/tools/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /export/data1/tools/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 mri_convert /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw/MRDC.00001 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig/001.mgz mri_convert /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw/MRDC.00001 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw/MRDC.00001... Starting DICOMRead2() dcmfile = /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw/MRDC.00001 dcmdir = /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mprage1mmiso20.83bw Ref Series No = 2 Found 182 files, checking for dicoms Found 180 dicom files in series. First Sorting Computing Slice Direction Vs: -1 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 180 ndcmfiles = 180 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=8.60, TE=3.83, TI=40.00, flip angle=8.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig/001.mgz... #------------------------------------------ recon-all -s NF108_11 finished without error at Wed Aug 17 13:37:58 EDT 2011 New invocation of recon-all Wed Aug 17 13:44:41 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 /export/data1/tools/freesurfer/bin/recon-all -s NF108_11 -all subjid NF108_11 setenv SUBJECTS_DIR /export/data1/tools/freesurfer/subjects/hannahas FREESURFER_HOME /export/data1/tools/freesurfer Actual FREESURFER_HOME /export/data1/tools/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16466344 13841756 2624588 0 240560 11919840 -/+ buffers/cache: 1681356 14784988 Swap: 18579448 0 18579448 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:41-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:42-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2011/08/17-17:44:43-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: hannahas Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /export/data1/tools/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /export/data1/tools/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Aug 17 13:44:43 EDT 2011 Found 1 runs /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig/001.mgz 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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig/001.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/rawavg.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 mri_convert /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/rawavg.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig.mgz --conform mri_convert /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/rawavg.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/rawavg.mgz... TR=8.60, TE=3.83, TI=40.00, flip angle=8.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig.mgz... mri_add_xform_to_header -c /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/transforms/talairach.xfm /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Wed Aug 17 13:44:56 EDT 2011 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri /export/data1/tools/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 17 13:44:56 EDT 2011 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.23499 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23499/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23499/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=8.60, TE=3.83, TI=40.00, flip angle=8.00 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.23499/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Aug 17 13:44:59 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23499/nu0.mnc ./tmp.mri_nu_correct.mni.23499/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23499/0/ [hannahas@localhost.localdomain:/export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/] [2011-08-17 13:44:59] running: /export/data1/tools/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23499/0/ ./tmp.mri_nu_correct.mni.23499/nu0.mnc ./tmp.mri_nu_correct.mni.23499/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000997831 [hannahas@localhost.localdomain:/export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/] [2011-08-17 13:45:24] running: /export/data1/tools/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23499/nu0.mnc ./tmp.mri_nu_correct.mni.23499/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Aug 17 13:45:27 EDT 2011 nu_correct -clobber ./tmp.mri_nu_correct.mni.23499/nu1.mnc ./tmp.mri_nu_correct.mni.23499/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23499/1/ [hannahas@localhost.localdomain:/export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/] [2011-08-17 13:45:27] running: /export/data1/tools/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23499/1/ ./tmp.mri_nu_correct.mni.23499/nu1.mnc ./tmp.mri_nu_correct.mni.23499/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 42 CV of field change: 0.000967855 [hannahas@localhost.localdomain:/export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/] [2011-08-17 13:45:53] running: /export/data1/tools/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23499/nu1.mnc ./tmp.mri_nu_correct.mni.23499/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.23499/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23499/ones.mgz $Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $ cwd /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23499/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23499/ones.mgz sysname Linux hostname localhost.localdomain machine x86_64 user hannahas input ./tmp.mri_nu_correct.mni.23499/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23499/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23499/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23499/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23499/input.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23499/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23499/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23499/input.mean.dat sysname Linux hostname localhost.localdomain machine x86_64 user hannahas Loading ./tmp.mri_nu_correct.mni.23499/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.23499/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23499/ones.mgz --i ./tmp.mri_nu_correct.mni.23499/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23499/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23499/output.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23499/ones.mgz --i ./tmp.mri_nu_correct.mni.23499/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23499/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23499/output.mean.dat sysname Linux hostname localhost.localdomain machine x86_64 user hannahas Loading ./tmp.mri_nu_correct.mni.23499/ones.mgz Loading ./tmp.mri_nu_correct.mni.23499/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.23499/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.23499/nu2.mnc ./tmp.mri_nu_correct.mni.23499/nu2.mnc mul .96068023046313481008 Saving result to './tmp.mri_nu_correct.mni.23499/nu2.mnc' (type=3) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.23499/nu2.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.23499/nu2.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.23499/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) 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 INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to nu.mgz... Wed Aug 17 13:46:42 EDT 2011 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Wed Aug 17 13:46:42 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Aug 17 13:48:10 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6775, pval=0.4932 >= threshold=0.0050) awk -f /export/data1/tools/freesurfer/bin/extract_talairach_avi_QA.awk /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/transforms/talairach_avi.log TalAviQA: 0.97607 z-score: 0 #-------------------------------------------- #@# Intensity Normalization Wed Aug 17 13:48:10 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.098 -0.072 -0.081 -1.820; 0.101 0.947 0.331 -29.926; 0.040 -0.295 1.091 27.882; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 13 seconds. MRIsplineNormalize(): npeaks = 12 Starting OpenSpline(): npoints = 12 white matter peak found at 111 white matter peak found at 108 gm peak at 62 (62), valley at 42 (42) csf peak at 31, setting threshold to 51 white matter peak found at 111 white matter peak found at 110 gm peak at 61 (61), valley at 39 (39) csf peak at 31, setting threshold to 51 #-------------------------------------------- #@# Skull Stripping Wed Aug 17 13:50:24 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_em_register -skull nu.mgz /export/data1/tools/freesurfer/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 '/export/data1/tools/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=19.0 skull bounding box = (58, 33, 17) --> (212, 255, 241) using (109, 107, 129) as brain centroid... mean wm in atlas = 126, using box (90,80,101) --> (127, 134,156) to find MRI wm before smoothing, mri peak at 162 after smoothing, mri peak at 162, scaling input intensities by 0.778 scaling channel 0 by 0.777778 initial log_p = -10404.6 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-5.1, 16.5, -1.7): log p = -10319.1 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10282.9, old_max_log_p =-10319.1 (thresh=-10308.7) 1.140 -0.034 0.126 -33.506; 0.000 1.111 0.298 -27.186; -0.150 -0.257 0.958 49.351; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10282.9, old_max_log_p =-10282.9 (thresh=-10272.7) 1.140 -0.034 0.126 -33.506; 0.000 1.111 0.298 -27.186; -0.150 -0.257 0.958 49.351; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10270.0, old_max_log_p =-10282.9 (thresh=-10272.7) 1.147 -0.055 0.054 -24.398; 0.033 1.079 0.326 -33.045; -0.079 -0.298 0.972 44.785; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10270.0, old_max_log_p =-10270.0 (thresh=-10259.7) 1.147 -0.055 0.054 -24.398; 0.033 1.079 0.326 -33.045; -0.079 -0.298 0.972 44.785; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10266.7, old_max_log_p =-10270.0 (thresh=-10259.7) 1.148 -0.064 0.051 -23.305; 0.041 1.074 0.333 -34.403; -0.079 -0.308 0.970 45.975; 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 1.14779 -0.06378 0.05140 -23.30482; 0.04150 1.07351 0.33323 -34.40285; -0.07935 -0.30765 0.97019 45.97514; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.14779 -0.06378 0.05140 -23.30482; 0.04150 1.07351 0.33323 -34.40285; -0.07935 -0.30765 0.97019 45.97514; 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) = 10266.7 tol 0.000010 Resulting transform: 1.148 -0.064 0.051 -23.305; 0.041 1.074 0.333 -34.403; -0.079 -0.308 0.970 45.975; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10266.7 (old=-10404.6) transform before final EM align: 1.148 -0.064 0.051 -23.305; 0.041 1.074 0.333 -34.403; -0.079 -0.308 0.970 45.975; 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 1.14779 -0.06378 0.05140 -23.30482; 0.04150 1.07351 0.33323 -34.40285; -0.07935 -0.30765 0.97019 45.97514; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.14779 -0.06378 0.05140 -23.30482; 0.04150 1.07351 0.33323 -34.40285; -0.07935 -0.30765 0.97019 45.97514; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 1143934.8 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.04, 1.07, 0.33, -34.40) ( -0.08, -0.31, 0.97, 45.98) 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 TOLERANCESpass 2 through quasi-newton minimization... dfp_em_step_func: 009: -log(p) = 1143866.9 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.97, 45.98) dfp_em_step_func: 010: -log(p) = 1143864.0 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.97, 45.98) dfp_em_step_func: 011: -log(p) = 1143854.4 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.96, 45.98) dfp_em_step_func: 012: -log(p) = 1143853.9 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.96, 45.98) dfp_em_step_func: 013: -log(p) = 1143853.2 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.96, 45.98) dfp_em_step_func: 014: -log(p) = 1143853.0 after pass:transform: ( 1.15, -0.06, 0.05, -23.30) ( 0.05, 1.08, 0.34, -34.40) ( -0.08, -0.31, 0.96, 45.98) 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 TOLERANCESpass 3 through quasi-newton minimization... 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: 016: -log(p) = 1143853.0 tol 0.000000 final transform: 1.147 -0.064 0.053 -23.305; 0.050 1.081 0.340 -34.403; -0.085 -0.312 0.964 45.975; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 26 minutes and 29 seconds. mri_watershed -T1 -brain_atlas /export/data1/tools/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=89 z=112 r=91 first estimation of the main basin volume: 3223986 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=151, y=81, z=78, Imax=255 CSF=14, 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=10027549011 voxels, voxel volume =1.000 = 10027549011 mmm3 = 10027548.672 cm3 done. PostAnalyze...Basin Prior 58 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=130,y=105, z=106, r=9958 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=9, CSF_MAX=48 , nb = 44748 RIGHT_CER CSF_MIN=2, CSF_intensity=12, CSF_MAX=36 , nb = 2826 LEFT_CER CSF_MIN=2, CSF_intensity=11, CSF_MAX=42 , nb = 2952 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=51 , nb = 19476 LEFT_BRAIN CSF_MIN=1, CSF_intensity=9, CSF_MAX=47 , nb = 19152 OTHER CSF_MIN=6, CSF_intensity=14, CSF_MAX=47 , nb = 342 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 48, 43, 41, 59 after analyzing : 34, 43, 43, 47 RIGHT_CER before analyzing : 36, 47, 52, 61 after analyzing : 36, 50, 52, 52 LEFT_CER before analyzing : 42, 37, 34, 59 after analyzing : 30, 37, 37, 42 RIGHT_BRAIN before analyzing : 51, 44, 41, 59 after analyzing : 35, 44, 44, 47 LEFT_BRAIN before analyzing : 47, 42, 41, 59 after analyzing : 33, 42, 42, 46 OTHER before analyzing : 47, 68, 71, 75 after analyzing : 47, 70, 71, 71 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...76 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 70.103, std = 9.114 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.17, sigma = 3.46 after rotation: sse = 2.17, sigma = 3.46 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.21, its var is 2.97 before Erosion-Dilatation 0.13% 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...43 iterations mri_strip_skull: done peeling brain Brain Size = 1698938 voxels, voxel volume = 1.000 mm3 = 1698938 mmm3 = 1698.938 cm3 ****************************** Saving brainmask.auto.mgz done mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz reading mask... white mean: 107.264767 threshold set to: 107.264767*0.360000=38.615316 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Aug 17 14:18:09 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_em_register -mask brainmask.mgz nu.mgz /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, 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=25.0 skull bounding box = (61, 42, 27) --> (200, 181, 202) using (107, 88, 115) as brain centroid... mean wm in atlas = 107, using box (90,71,93) --> (124, 105,136) to find MRI wm before smoothing, mri peak at 162 after smoothing, mri peak at 162, scaling input intensities by 0.660 scaling channel 0 by 0.660494 initial log_p = -6291.7 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-5.1, 18.7, -5.1): log p = -5892.4 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-5665.2, old_max_log_p =-5892.4 (thresh=-5886.5) 1.140 -0.052 0.120 -31.601; 0.000 1.068 0.421 -34.525; -0.150 -0.398 0.911 71.884; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-5665.2, old_max_log_p =-5665.2 (thresh=-5659.6) 1.140 -0.052 0.120 -31.601; 0.000 1.068 0.421 -34.525; -0.150 -0.398 0.911 71.884; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-5575.2, old_max_log_p =-5665.2 (thresh=-5659.6) 1.186 -0.081 0.084 -30.839; 0.053 1.079 0.325 -32.907; -0.105 -0.284 0.916 49.905; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-5574.6, old_max_log_p =-5575.2 (thresh=-5569.6) 1.165 -0.045 0.092 -32.612; 0.017 1.090 0.292 -25.774; -0.105 -0.253 0.943 43.837; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5547.7, old_max_log_p =-5574.6 (thresh=-5569.0) 1.165 -0.058 0.071 -29.502; 0.035 1.089 0.302 -29.629; -0.086 -0.261 0.939 42.638; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-5544.4, old_max_log_p =-5547.7 (thresh=-5542.1) 1.166 -0.049 0.074 -30.901; 0.025 1.086 0.309 -29.148; -0.086 -0.271 0.937 43.314; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16620 -0.04920 0.07381 -30.90074; 0.02509 1.08644 0.30871 -29.14838; -0.08633 -0.27072 0.93728 43.31379; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.16620 -0.04920 0.07381 -30.90074; 0.02509 1.08644 0.30871 -29.14838; -0.08633 -0.27072 0.93728 43.31379; 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: 008: -log(p) = 5544.4 tol 0.000010 Resulting transform: 1.166 -0.049 0.074 -30.901; 0.025 1.086 0.309 -29.148; -0.086 -0.271 0.937 43.314; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -5544.4 (old=-6291.7) transform before final EM align: 1.166 -0.049 0.074 -30.901; 0.025 1.086 0.309 -29.148; -0.086 -0.271 0.937 43.314; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16620 -0.04920 0.07381 -30.90074; 0.02509 1.08644 0.30871 -29.14838; -0.08633 -0.27072 0.93728 43.31379; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.16620 -0.04920 0.07381 -30.90074; 0.02509 1.08644 0.30871 -29.14838; -0.08633 -0.27072 0.93728 43.31379; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 009: -log(p) = 679368.4 after pass:transform: ( 1.17, -0.05, 0.07, -30.90) ( 0.03, 1.09, 0.31, -29.15) ( -0.09, -0.27, 0.94, 43.31) dfp_em_step_func: 010: -log(p) = 677277.8 after pass:transform: ( 1.17, -0.04, 0.08, -30.90) ( 0.03, 1.09, 0.31, -29.15) ( -0.08, -0.27, 0.94, 43.31) 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 TOLERANCESpass 2 through quasi-newton minimization... 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: 012: -log(p) = 677277.8 tol 0.000000 final transform: 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 18 minutes and 48 seconds. #-------------------------------------- #@# CA Normalize Wed Aug 17 14:36:58 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=25.0 skull bounding box = (61, 42, 27) --> (200, 181, 202) using (107, 88, 115) as brain centroid... mean wm in atlas = 107, using box (90,71,93) --> (124, 105,136) to find MRI wm before smoothing, mri peak at 162 after smoothing, mri peak at 162, scaling input intensities by 0.660 scaling channel 0 by 0.660494 using 244171 sample points... INFO: compute sample coordinates transform 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 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 (127, 43, 31) --> (187, 149, 196) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 152.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (74, 43, 28) --> (131, 143, 196) Right_Cerebral_White_Matter: limiting intensities to 117.0 --> 152.0 12 of 14 (85.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 124, 61) --> (175, 164, 114) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 152.0 0 of 10 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 124, 56) --> (134, 165, 113) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 152.0 0 of 12 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 113, 94) --> (144, 175, 124) Brain_Stem: limiting intensities to 81.0 --> 152.0 0 of 7 (0.0%) samples deleted using 51 total control points for intensity normalization... bias field = 0.972 +- 0.041 0 of 39 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 43, 31) --> (187, 149, 196) Left_Cerebral_White_Matter: limiting intensities to 99.0 --> 155.0 0 of 91 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (74, 43, 28) --> (131, 143, 196) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 155.0 0 of 66 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 124, 61) --> (175, 164, 114) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 155.0 0 of 39 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 124, 56) --> (134, 165, 113) Right_Cerebellum_White_Matter: limiting intensities to 80.0 --> 155.0 0 of 38 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 113, 94) --> (144, 175, 124) Brain_Stem: limiting intensities to 79.0 --> 155.0 7 of 53 (13.2%) samples deleted using 287 total control points for intensity normalization... bias field = 0.983 +- 0.044 0 of 280 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 43, 31) --> (187, 149, 196) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 150.0 0 of 219 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (74, 43, 28) --> (131, 143, 196) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 150.0 0 of 178 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (134, 124, 61) --> (175, 164, 114) Left_Cerebellum_White_Matter: limiting intensities to 77.0 --> 150.0 2 of 51 (3.9%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 124, 56) --> (134, 165, 113) Right_Cerebellum_White_Matter: limiting intensities to 79.0 --> 150.0 0 of 47 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 113, 94) --> (144, 175, 124) Brain_Stem: limiting intensities to 73.0 --> 150.0 0 of 137 (0.0%) samples deleted using 632 total control points for intensity normalization... bias field = 1.009 +- 0.045 0 of 630 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Wed Aug 17 14:38:41 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/export/data1/tools/freesurfer/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) = 1.31 (predicted orig area = 6.1) 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=0.752, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40431.652 ms 0001: dt=238.698565, rms=0.711 (5.548%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40593.004 ms 0002: dt=199.917526, rms=0.697 (1.971%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40727.094 ms 0003: dt=183.222857, rms=0.686 (1.522%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41682.445 ms 0004: dt=135.783784, rms=0.681 (0.774%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40292.789 ms 0005: dt=295.936000, rms=0.673 (1.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40597.836 ms 0006: dt=70.374502, rms=0.671 (0.403%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40656.906 ms 0007: dt=517.888000, rms=0.665 (0.773%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40901.527 ms 0008: dt=129.472000, rms=0.662 (0.566%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38450.324 ms 0009: dt=73.984000, rms=0.661 (0.074%), neg=0, invalid=766 0010: dt=73.984000, rms=0.660 (0.093%), neg=0, invalid=766 0011: dt=73.984000, rms=0.659 (0.157%), neg=0, invalid=766 0012: dt=73.984000, rms=0.658 (0.200%), neg=0, invalid=766 0013: dt=73.984000, rms=0.657 (0.242%), neg=0, invalid=766 0014: dt=73.984000, rms=0.655 (0.284%), neg=0, invalid=766 0015: dt=73.984000, rms=0.653 (0.311%), neg=0, invalid=766 0016: dt=73.984000, rms=0.651 (0.300%), neg=0, invalid=766 0017: dt=73.984000, rms=0.649 (0.288%), neg=0, invalid=766 0018: dt=73.984000, rms=0.647 (0.260%), neg=0, invalid=766 0019: dt=73.984000, rms=0.645 (0.250%), neg=0, invalid=766 0020: dt=73.984000, rms=0.644 (0.247%), neg=0, invalid=766 0021: dt=73.984000, rms=0.642 (0.238%), neg=0, invalid=766 0022: dt=73.984000, rms=0.641 (0.197%), neg=0, invalid=766 0023: dt=73.984000, rms=0.640 (0.186%), neg=0, invalid=766 0024: dt=73.984000, rms=0.639 (0.157%), neg=0, invalid=766 0025: dt=73.984000, rms=0.638 (0.152%), neg=0, invalid=766 0026: dt=73.984000, rms=0.637 (0.164%), neg=0, invalid=766 0027: dt=73.984000, rms=0.636 (0.144%), neg=0, invalid=766 0028: dt=73.984000, rms=0.635 (0.126%), neg=0, invalid=766 0029: dt=73.984000, rms=0.634 (0.124%), neg=0, invalid=766 0030: dt=73.984000, rms=0.634 (0.125%), neg=0, invalid=766 0031: dt=73.984000, rms=0.633 (0.128%), neg=0, invalid=766 0032: dt=73.984000, rms=0.632 (0.122%), neg=0, invalid=766 0033: dt=73.984000, rms=0.631 (0.120%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40562.781 ms 0034: dt=1183.744000, rms=0.630 (0.164%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40599.461 ms 0035: dt=32.368000, rms=0.630 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.630, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45215.191 ms 0036: dt=32.368000, rms=0.630 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50752.531 ms 0037: dt=32.368000, rms=0.630 (0.013%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47600.445 ms 0038: dt=73.984000, rms=0.630 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44482.254 ms 0039: dt=443.904000, rms=0.629 (0.103%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42304.797 ms 0040: dt=129.472000, rms=0.629 (0.041%), neg=0, invalid=766 0041: dt=129.472000, rms=0.629 (0.040%), neg=0, invalid=766 0042: dt=129.472000, rms=0.629 (0.028%), neg=0, invalid=766 0043: dt=129.472000, rms=0.629 (0.009%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.635, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42706.164 ms 0044: dt=213.917808, rms=0.620 (2.340%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41534.328 ms 0045: dt=46.920245, rms=0.615 (0.840%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45411.746 ms 0046: dt=93.313697, rms=0.608 (1.092%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40673.578 ms 0047: dt=15.807229, rms=0.607 (0.204%), neg=0, invalid=766 0048: dt=15.807229, rms=0.606 (0.070%), neg=0, invalid=766 0049: dt=15.807229, rms=0.606 (0.008%), neg=0, invalid=766 0050: dt=15.807229, rms=0.605 (0.159%), neg=0, invalid=766 0051: dt=15.807229, rms=0.603 (0.404%), neg=0, invalid=766 0052: dt=15.807229, rms=0.600 (0.541%), neg=0, invalid=766 0053: dt=15.807229, rms=0.597 (0.502%), neg=0, invalid=766 0054: dt=15.807229, rms=0.594 (0.396%), neg=0, invalid=766 0055: dt=15.807229, rms=0.592 (0.326%), neg=0, invalid=766 0056: dt=15.807229, rms=0.591 (0.264%), neg=0, invalid=766 0057: dt=15.807229, rms=0.589 (0.299%), neg=0, invalid=766 0058: dt=15.807229, rms=0.587 (0.390%), neg=0, invalid=766 0059: dt=15.807229, rms=0.584 (0.434%), neg=0, invalid=766 0060: dt=15.807229, rms=0.582 (0.351%), neg=0, invalid=766 0061: dt=15.807229, rms=0.581 (0.269%), neg=0, invalid=766 0062: dt=15.807229, rms=0.579 (0.207%), neg=0, invalid=766 0063: dt=15.807229, rms=0.578 (0.159%), neg=0, invalid=766 0064: dt=15.807229, rms=0.577 (0.165%), neg=0, invalid=766 0065: dt=15.807229, rms=0.576 (0.215%), neg=0, invalid=766 0066: dt=15.807229, rms=0.575 (0.228%), neg=0, invalid=766 0067: dt=15.807229, rms=0.574 (0.195%), neg=0, invalid=766 0068: dt=15.807229, rms=0.573 (0.149%), neg=0, invalid=766 0069: dt=15.807229, rms=0.572 (0.101%), neg=0, invalid=766 0070: dt=15.807229, rms=0.572 (0.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40634.586 ms 0071: dt=50.666667, rms=0.571 (0.089%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38692.715 ms 0072: dt=1.666667, rms=0.571 (-0.004%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.571, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44396.715 ms 0073: dt=9.072000, rms=0.571 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45356.699 ms 0074: dt=9.072000, rms=0.571 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38753.762 ms 0075: dt=25.920000, rms=0.571 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45115.656 ms 0076: dt=82.944000, rms=0.571 (0.035%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44746.590 ms 0077: dt=2.268000, rms=0.571 (-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=0.597, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39862.484 ms 0078: dt=10.260870, rms=0.596 (0.190%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40321.684 ms 0079: dt=6.693878, rms=0.596 (0.035%), neg=0, invalid=766 0080: dt=6.693878, rms=0.596 (0.007%), neg=0, invalid=766 0081: dt=6.693878, rms=0.596 (-0.065%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.596, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37474.012 ms 0082: dt=0.000000, rms=0.596 (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=0.656, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37512.156 ms 0083: dt=5.588889, rms=0.645 (1.664%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37628.809 ms 0084: dt=3.456000, rms=0.644 (0.105%), neg=0, invalid=766 0085: dt=3.456000, rms=0.644 (-0.011%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.644, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38294.770 ms 0086: dt=0.000000, rms=0.644 (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=0.710, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38525.504 ms 0087: dt=0.876833, rms=0.708 (0.297%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38245.980 ms 0088: dt=2.536364, rms=0.702 (0.790%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43630.344 ms 0089: dt=2.000000, rms=0.700 (0.292%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41626.719 ms 0090: dt=1.708955, rms=0.697 (0.433%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38002.629 ms 0091: dt=0.320000, rms=0.697 (0.022%), neg=0, invalid=766 0092: dt=0.320000, rms=0.697 (0.006%), neg=0, invalid=766 0093: dt=0.320000, rms=0.697 (-0.008%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38544.598 ms 0094: dt=1.100917, rms=0.696 (0.140%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38573.570 ms 0095: dt=1.024000, rms=0.696 (0.042%), neg=0, invalid=766 0096: dt=1.024000, rms=0.696 (0.046%), neg=0, invalid=766 0097: dt=1.024000, rms=0.695 (0.032%), neg=0, invalid=766 0098: dt=1.024000, rms=0.695 (-0.034%), 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=0.655, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38281.848 ms 0099: dt=0.797561, rms=0.639 (2.410%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33571.531 ms 0100: dt=0.028000, rms=0.638 (0.167%), neg=0, invalid=766 0101: dt=0.028000, rms=0.638 (-0.053%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35959.648 ms 0102: dt=0.020000, rms=0.638 (0.034%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33332.223 ms 0103: dt=0.000000, rms=0.638 (-0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.04088 (18) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (3053 voxels, overlap=0.000) Left_Lateral_Ventricle (4): linear fit = 0.65 x + 0.0 (3053 voxels, peak = 16), gca=15.6 gca peak = 0.14022 (22) mri peak = 0.04859 (18) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (2511 voxels, overlap=0.279) Right_Lateral_Ventricle (43): linear fit = 0.73 x + 0.0 (2511 voxels, peak = 16), gca=16.0 gca peak = 0.24234 (100) mri peak = 0.07135 (86) Right_Pallidum (52): linear fit = 0.85 x + 0.0 (461 voxels, overlap=0.001) Right_Pallidum (52): linear fit = 0.85 x + 0.0 (461 voxels, peak = 85), gca=85.0 gca peak = 0.19192 (97) mri peak = 0.08561 (84) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (414 voxels, overlap=0.315) Left_Pallidum (13): linear fit = 0.85 x + 0.0 (414 voxels, peak = 82), gca=82.5 gca peak = 0.24007 (63) mri peak = 0.07659 (63) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (977 voxels, overlap=0.948) Right_Hippocampus (53): linear fit = 0.98 x + 0.0 (977 voxels, peak = 61), gca=61.4 gca peak = 0.29892 (64) mri peak = 0.06944 (62) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (961 voxels, overlap=0.961) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (961 voxels, peak = 61), gca=60.8 gca peak = 0.12541 (104) mri peak = 0.05891 (105) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (80533 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (80533 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.05048 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84807 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (84807 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03123 (68) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (50916 voxels, overlap=0.808) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (50916 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.03103 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (50599 voxels, overlap=0.951) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (50599 voxels, peak = 63), gca=63.0 gca peak = 0.15182 (70) mri peak = 0.13417 (70) Right_Caudate (50): linear fit = 0.98 x + 0.0 (635 voxels, overlap=0.866) Right_Caudate (50): linear fit = 0.98 x + 0.0 (635 voxels, peak = 68), gca=68.2 gca peak = 0.14251 (76) mri peak = 0.12437 (74) Left_Caudate (11): linear fit = 0.93 x + 0.0 (759 voxels, overlap=0.386) Left_Caudate (11): linear fit = 0.93 x + 0.0 (759 voxels, peak = 70), gca=70.3 gca peak = 0.12116 (60) mri peak = 0.04087 (67) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (35180 voxels, overlap=0.949) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (35180 voxels, peak = 64), gca=64.5 gca peak = 0.12723 (61) mri peak = 0.04302 (68) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (38558 voxels, overlap=0.940) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (38558 voxels, peak = 66), gca=65.6 gca peak = 0.22684 (88) mri peak = 0.06038 (89) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9977 voxels, overlap=0.925) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (9977 voxels, peak = 92), gca=92.4 gca peak = 0.21067 (87) mri peak = 0.06991 (86) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8715 voxels, overlap=0.933) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (8715 voxels, peak = 89), gca=89.2 gca peak = 0.25455 (62) mri peak = 0.08322 (58) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, overlap=0.805) Left_Amygdala (18): linear fit = 0.88 x + 0.0 (350 voxels, peak = 54), gca=54.2 gca peak = 0.39668 (62) mri peak = 0.09264 (56) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (350 voxels, overlap=0.534) Right_Amygdala (54): linear fit = 0.90 x + 0.0 (350 voxels, peak = 56), gca=55.8 gca peak = 0.10129 (93) mri peak = 0.04582 (78) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (5139 voxels, overlap=0.590) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (5139 voxels, peak = 84), gca=83.7 gca peak = 0.12071 (89) mri peak = 0.06433 (83) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (4600 voxels, overlap=0.867) Right_Thalamus_Proper (49): linear fit = 0.93 x + 0.0 (4600 voxels, peak = 82), gca=82.3 gca peak = 0.13716 (82) mri peak = 0.05482 (83) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2542 voxels, overlap=0.954) Left_Putamen (12): linear fit = 0.98 x + 0.0 (2542 voxels, peak = 80), gca=80.0 gca peak = 0.15214 (84) mri peak = 0.05982 (75) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2494 voxels, overlap=0.699) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2494 voxels, peak = 78), gca=77.7 gca peak = 0.08983 (85) mri peak = 0.05217 (88) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13678 voxels, overlap=0.821) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13678 voxels, peak = 89), gca=89.2 gca peak = 0.11809 (92) mri peak = 0.04343 (83) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1396 voxels, overlap=0.562) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1396 voxels, peak = 94), gca=94.3 gca peak = 0.12914 (94) mri peak = 0.04582 (92) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1601 voxels, overlap=0.704) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1601 voxels, peak = 92), gca=91.7 gca peak = 0.21100 (36) mri peak = 0.06661 (27) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (127 voxels, overlap=0.229) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (127 voxels, peak = 30), gca=29.7 gca peak = 0.13542 (27) mri peak = 0.05950 (27) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (734 voxels, overlap=0.846) Fourth_Ventricle (15): linear fit = 1.10 x + 0.0 (734 voxels, peak = 30), gca=29.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 0.95 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.83 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=0.651, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44048.457 ms 0104: dt=146.285714, rms=0.645 (0.941%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44122.867 ms 0105: dt=182.979866, rms=0.640 (0.727%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44834.980 ms 0106: dt=62.819188, rms=0.639 (0.160%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41541.203 ms 0107: dt=517.888000, rms=0.635 (0.574%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44232.781 ms 0108: dt=97.240310, rms=0.634 (0.203%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42262.469 ms 0109: dt=369.920000, rms=0.631 (0.431%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42338.570 ms 0110: dt=32.368000, rms=0.631 (0.086%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39932.973 ms 0111: dt=32.368000, rms=0.631 (0.021%), neg=0, invalid=766 0112: dt=32.368000, rms=0.631 (0.020%), neg=0, invalid=766 0113: dt=32.368000, rms=0.630 (0.026%), neg=0, invalid=766 0114: dt=32.368000, rms=0.630 (0.045%), neg=0, invalid=766 0115: dt=32.368000, rms=0.630 (0.076%), neg=0, invalid=766 0116: dt=32.368000, rms=0.629 (0.113%), neg=0, invalid=766 0117: dt=32.368000, rms=0.628 (0.131%), neg=0, invalid=766 0118: dt=32.368000, rms=0.627 (0.126%), neg=0, invalid=766 0119: dt=32.368000, rms=0.627 (0.111%), neg=0, invalid=766 0120: dt=32.368000, rms=0.626 (0.100%), neg=0, invalid=766 0121: dt=32.368000, rms=0.625 (0.092%), neg=0, invalid=766 0122: dt=32.368000, rms=0.625 (0.087%), neg=0, invalid=766 0123: dt=32.368000, rms=0.624 (0.092%), neg=0, invalid=766 0124: dt=32.368000, rms=0.624 (0.098%), neg=0, invalid=766 0125: dt=32.368000, rms=0.623 (0.099%), neg=0, invalid=766 0126: dt=32.368000, rms=0.623 (0.095%), neg=0, invalid=766 0127: dt=32.368000, rms=0.622 (0.082%), neg=0, invalid=766 0128: dt=32.368000, rms=0.622 (0.064%), neg=0, invalid=766 0129: dt=32.368000, rms=0.621 (0.058%), neg=0, invalid=766 0130: dt=32.368000, rms=0.621 (0.052%), neg=0, invalid=766 0131: dt=32.368000, rms=0.621 (0.050%), neg=0, invalid=766 0132: dt=32.368000, rms=0.620 (0.047%), neg=0, invalid=766 0133: dt=32.368000, rms=0.620 (0.047%), neg=0, invalid=766 0134: dt=32.368000, rms=0.620 (0.045%), neg=0, invalid=766 0135: dt=32.368000, rms=0.620 (0.041%), neg=0, invalid=766 0136: dt=32.368000, rms=0.619 (0.040%), neg=0, invalid=766 0137: dt=32.368000, rms=0.619 (0.036%), neg=0, invalid=766 0138: dt=32.368000, rms=0.619 (0.032%), neg=0, invalid=766 0139: dt=32.368000, rms=0.619 (0.031%), neg=0, invalid=766 0140: dt=32.368000, rms=0.618 (0.033%), neg=0, invalid=766 0141: dt=32.368000, rms=0.618 (0.045%), neg=0, invalid=766 0142: dt=32.368000, rms=0.618 (0.046%), neg=0, invalid=766 0143: dt=32.368000, rms=0.618 (0.048%), neg=0, invalid=766 0144: dt=32.368000, rms=0.617 (0.047%), neg=0, invalid=766 0145: dt=32.368000, rms=0.617 (0.043%), neg=0, invalid=766 0146: dt=32.368000, rms=0.617 (0.041%), neg=0, invalid=766 0147: dt=32.368000, rms=0.617 (0.034%), neg=0, invalid=766 0148: dt=32.368000, rms=0.616 (0.030%), neg=0, invalid=766 0149: dt=32.368000, rms=0.616 (0.033%), neg=0, invalid=766 0150: dt=32.368000, rms=0.616 (0.038%), neg=0, invalid=766 0151: dt=32.368000, rms=0.616 (0.041%), neg=0, invalid=766 0152: dt=32.368000, rms=0.615 (0.044%), neg=0, invalid=766 0153: dt=32.368000, rms=0.615 (0.040%), neg=0, invalid=766 0154: dt=32.368000, rms=0.615 (0.034%), neg=0, invalid=766 0155: dt=32.368000, rms=0.615 (0.030%), neg=0, invalid=766 0156: dt=32.368000, rms=0.615 (0.034%), neg=0, invalid=766 0157: dt=32.368000, rms=0.614 (0.036%), neg=0, invalid=766 0158: dt=32.368000, rms=0.614 (0.039%), neg=0, invalid=766 0159: dt=32.368000, rms=0.614 (0.041%), neg=0, invalid=766 0160: dt=32.368000, rms=0.614 (0.043%), neg=0, invalid=766 0161: dt=32.368000, rms=0.613 (0.041%), neg=0, invalid=766 0162: dt=32.368000, rms=0.613 (0.037%), neg=0, invalid=766 0163: dt=32.368000, rms=0.613 (0.039%), neg=0, invalid=766 0164: dt=32.368000, rms=0.613 (0.036%), neg=0, invalid=766 0165: dt=32.368000, rms=0.612 (0.036%), neg=0, invalid=766 0166: dt=32.368000, rms=0.612 (0.035%), neg=0, invalid=766 0167: dt=32.368000, rms=0.612 (0.032%), neg=0, invalid=766 0168: dt=32.368000, rms=0.612 (0.033%), neg=0, invalid=766 0169: dt=32.368000, rms=0.612 (0.032%), neg=0, invalid=766 0170: dt=32.368000, rms=0.611 (0.030%), neg=0, invalid=766 0171: dt=32.368000, rms=0.611 (0.028%), neg=0, invalid=766 0172: dt=32.368000, rms=0.611 (0.030%), neg=0, invalid=766 0173: dt=32.368000, rms=0.611 (0.031%), neg=0, invalid=766 0174: dt=32.368000, rms=0.611 (0.034%), neg=0, invalid=766 0175: dt=32.368000, rms=0.611 (0.033%), neg=0, invalid=766 0176: dt=32.368000, rms=0.610 (0.032%), neg=0, invalid=766 0177: dt=32.368000, rms=0.610 (0.030%), neg=0, invalid=766 0178: dt=32.368000, rms=0.610 (0.030%), neg=0, invalid=766 0179: dt=32.368000, rms=0.610 (0.028%), neg=0, invalid=766 0180: dt=32.368000, rms=0.610 (0.028%), neg=0, invalid=766 0181: dt=32.368000, rms=0.609 (0.027%), neg=0, invalid=766 0182: dt=32.368000, rms=0.609 (0.026%), neg=0, invalid=766 0183: dt=32.368000, rms=0.609 (0.027%), neg=0, invalid=766 0184: dt=32.368000, rms=0.609 (0.022%), neg=0, invalid=766 0185: dt=32.368000, rms=0.609 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46009.840 ms 0186: dt=1183.744000, rms=0.608 (0.076%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43135.797 ms 0187: dt=32.368000, rms=0.608 (0.012%), neg=0, invalid=766 0188: dt=32.368000, rms=0.608 (0.004%), neg=0, invalid=766 0189: dt=32.368000, rms=0.608 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.608, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40897.293 ms 0190: dt=110.976000, rms=0.608 (0.039%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 47073.859 ms 0191: dt=295.936000, rms=0.607 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43136.508 ms 0192: dt=32.368000, rms=0.607 (0.009%), neg=0, invalid=766 0193: dt=32.368000, rms=0.607 (0.001%), neg=0, invalid=766 0194: dt=32.368000, rms=0.607 (0.000%), neg=0, invalid=766 0195: dt=32.368000, rms=0.607 (-0.003%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.608, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40844.090 ms 0196: dt=133.132075, rms=0.601 (1.206%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40908.031 ms 0197: dt=61.714286, rms=0.595 (1.031%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43444.664 ms 0198: dt=62.208000, rms=0.591 (0.713%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39435.426 ms 0199: dt=36.288000, rms=0.589 (0.201%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40740.555 ms 0200: dt=131.023622, rms=0.583 (1.021%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38249.488 ms 0201: dt=17.726619, rms=0.582 (0.258%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38188.824 ms 0202: dt=9.333333, rms=0.582 (0.067%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40688.617 ms 0203: dt=36.288000, rms=0.581 (0.065%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40483.316 ms 0204: dt=189.658537, rms=0.576 (0.949%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38133.984 ms 0205: dt=25.920000, rms=0.574 (0.304%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38090.285 ms 0206: dt=9.072000, rms=0.574 (0.044%), neg=0, invalid=766 0207: dt=9.072000, rms=0.574 (0.015%), neg=0, invalid=766 0208: dt=9.072000, rms=0.573 (0.010%), neg=0, invalid=766 0209: dt=9.072000, rms=0.573 (0.049%), neg=0, invalid=766 0210: dt=9.072000, rms=0.573 (0.100%), neg=0, invalid=766 0211: dt=9.072000, rms=0.572 (0.174%), neg=0, invalid=766 0212: dt=9.072000, rms=0.570 (0.214%), neg=0, invalid=766 0213: dt=9.072000, rms=0.569 (0.216%), neg=0, invalid=766 0214: dt=9.072000, rms=0.568 (0.205%), neg=0, invalid=766 0215: dt=9.072000, rms=0.567 (0.194%), neg=0, invalid=766 0216: dt=9.072000, rms=0.566 (0.173%), neg=0, invalid=766 0217: dt=9.072000, rms=0.565 (0.159%), neg=0, invalid=766 0218: dt=9.072000, rms=0.564 (0.156%), neg=0, invalid=766 0219: dt=9.072000, rms=0.563 (0.162%), neg=0, invalid=766 0220: dt=9.072000, rms=0.562 (0.184%), neg=0, invalid=766 0221: dt=9.072000, rms=0.561 (0.202%), neg=0, invalid=766 0222: dt=9.072000, rms=0.560 (0.201%), neg=0, invalid=766 0223: dt=9.072000, rms=0.559 (0.181%), neg=0, invalid=766 0224: dt=9.072000, rms=0.558 (0.152%), neg=0, invalid=766 0225: dt=9.072000, rms=0.557 (0.138%), neg=0, invalid=766 0226: dt=9.072000, rms=0.557 (0.126%), neg=0, invalid=766 0227: dt=9.072000, rms=0.556 (0.117%), neg=0, invalid=766 0228: dt=9.072000, rms=0.555 (0.117%), neg=0, invalid=766 0229: dt=9.072000, rms=0.555 (0.130%), neg=0, invalid=766 0230: dt=9.072000, rms=0.554 (0.137%), neg=0, invalid=766 0231: dt=9.072000, rms=0.553 (0.145%), neg=0, invalid=766 0232: dt=9.072000, rms=0.552 (0.135%), neg=0, invalid=766 0233: dt=9.072000, rms=0.552 (0.121%), neg=0, invalid=766 0234: dt=9.072000, rms=0.551 (0.105%), neg=0, invalid=766 0235: dt=9.072000, rms=0.551 (0.087%), neg=0, invalid=766 0236: dt=9.072000, rms=0.550 (0.080%), neg=0, invalid=766 0237: dt=9.072000, rms=0.550 (0.091%), neg=0, invalid=766 0238: dt=9.072000, rms=0.549 (0.095%), neg=0, invalid=766 0239: dt=9.072000, rms=0.548 (0.106%), neg=0, invalid=766 0240: dt=9.072000, rms=0.548 (0.101%), neg=0, invalid=766 0241: dt=9.072000, rms=0.547 (0.097%), neg=0, invalid=766 0242: dt=9.072000, rms=0.547 (0.090%), neg=0, invalid=766 0243: dt=9.072000, rms=0.546 (0.083%), neg=0, invalid=766 0244: dt=9.072000, rms=0.546 (0.079%), neg=0, invalid=766 0245: dt=9.072000, rms=0.546 (0.076%), neg=0, invalid=766 0246: dt=9.072000, rms=0.545 (0.075%), neg=0, invalid=766 0247: dt=9.072000, rms=0.545 (0.080%), neg=0, invalid=766 0248: dt=9.072000, rms=0.544 (0.079%), neg=0, invalid=766 0249: dt=9.072000, rms=0.544 (0.075%), neg=0, invalid=766 0250: dt=9.072000, rms=0.544 (0.069%), neg=0, invalid=766 0251: dt=9.072000, rms=0.543 (0.065%), neg=0, invalid=766 0252: dt=9.072000, rms=0.543 (0.059%), neg=0, invalid=766 0253: dt=9.072000, rms=0.543 (0.061%), neg=0, invalid=766 0254: dt=9.072000, rms=0.542 (0.062%), neg=0, invalid=766 0255: dt=9.072000, rms=0.542 (0.060%), neg=0, invalid=766 0256: dt=9.072000, rms=0.542 (0.059%), neg=0, invalid=766 0257: dt=9.072000, rms=0.541 (0.059%), neg=0, invalid=766 0258: dt=9.072000, rms=0.541 (0.060%), neg=0, invalid=766 0259: dt=9.072000, rms=0.541 (0.056%), neg=0, invalid=766 0260: dt=9.072000, rms=0.540 (0.056%), neg=0, invalid=766 0261: dt=9.072000, rms=0.540 (0.053%), neg=0, invalid=766 0262: dt=9.072000, rms=0.540 (0.049%), neg=0, invalid=766 0263: dt=9.072000, rms=0.539 (0.052%), neg=0, invalid=766 0264: dt=9.072000, rms=0.539 (0.051%), neg=0, invalid=766 0265: dt=9.072000, rms=0.539 (0.049%), neg=0, invalid=766 0266: dt=9.072000, rms=0.539 (0.048%), neg=0, invalid=766 0267: dt=9.072000, rms=0.538 (0.051%), neg=0, invalid=766 0268: dt=9.072000, rms=0.538 (0.049%), neg=0, invalid=766 0269: dt=9.072000, rms=0.538 (0.048%), neg=0, invalid=766 0270: dt=9.072000, rms=0.538 (0.047%), neg=0, invalid=766 0271: dt=9.072000, rms=0.537 (0.047%), neg=0, invalid=766 0272: dt=9.072000, rms=0.537 (0.044%), neg=0, invalid=766 0273: dt=9.072000, rms=0.537 (0.045%), neg=0, invalid=766 0274: dt=9.072000, rms=0.537 (0.043%), neg=0, invalid=766 0275: dt=9.072000, rms=0.536 (0.043%), neg=0, invalid=766 0276: dt=9.072000, rms=0.536 (0.043%), neg=0, invalid=766 0277: dt=9.072000, rms=0.536 (0.045%), neg=0, invalid=766 0278: dt=9.072000, rms=0.536 (0.043%), neg=0, invalid=766 0279: dt=9.072000, rms=0.536 (0.042%), neg=0, invalid=766 0280: dt=9.072000, rms=0.535 (0.041%), neg=0, invalid=766 0281: dt=9.072000, rms=0.535 (0.037%), neg=0, invalid=766 0282: dt=9.072000, rms=0.535 (0.037%), neg=0, invalid=766 0283: dt=9.072000, rms=0.535 (0.037%), neg=0, invalid=766 0284: dt=9.072000, rms=0.535 (0.038%), neg=0, invalid=766 0285: dt=9.072000, rms=0.534 (0.038%), neg=0, invalid=766 0286: dt=9.072000, rms=0.534 (0.035%), neg=0, invalid=766 0287: dt=9.072000, rms=0.534 (0.037%), neg=0, invalid=766 0288: dt=9.072000, rms=0.534 (0.034%), neg=0, invalid=766 0289: dt=9.072000, rms=0.534 (0.032%), neg=0, invalid=766 0290: dt=9.072000, rms=0.533 (0.030%), neg=0, invalid=766 0291: dt=9.072000, rms=0.533 (0.029%), neg=0, invalid=766 0292: dt=9.072000, rms=0.533 (0.030%), neg=0, invalid=766 0293: dt=9.072000, rms=0.533 (0.031%), neg=0, invalid=766 0294: dt=9.072000, rms=0.533 (0.032%), neg=0, invalid=766 0295: dt=9.072000, rms=0.533 (0.029%), neg=0, invalid=766 0296: dt=9.072000, rms=0.532 (0.031%), neg=0, invalid=766 0297: dt=9.072000, rms=0.532 (0.027%), neg=0, invalid=766 0298: dt=9.072000, rms=0.532 (0.027%), neg=0, invalid=766 0299: dt=9.072000, rms=0.532 (0.024%), neg=0, invalid=766 0300: dt=9.072000, rms=0.532 (0.024%), neg=0, invalid=766 0301: dt=9.072000, rms=0.532 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40769.605 ms 0302: dt=580.608000, rms=0.531 (0.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38202.477 ms 0303: dt=9.072000, rms=0.531 (0.012%), neg=0, invalid=766 0304: dt=9.072000, rms=0.531 (0.007%), neg=0, invalid=766 0305: dt=9.072000, rms=0.531 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.531, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40697.156 ms 0306: dt=54.666667, rms=0.530 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40784.895 ms 0307: dt=93.000000, rms=0.529 (0.234%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38347.004 ms 0308: dt=10.000000, rms=0.529 (0.027%), neg=0, invalid=766 0309: dt=10.000000, rms=0.528 (0.014%), neg=0, invalid=766 0310: dt=10.000000, rms=0.528 (0.005%), neg=0, invalid=766 0311: dt=10.000000, rms=0.528 (-0.016%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.538, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40595.965 ms 0312: dt=56.626087, rms=0.533 (1.036%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38244.863 ms 0313: dt=29.147950, rms=0.526 (1.220%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38372.008 ms 0314: dt=15.780822, rms=0.524 (0.430%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38647.109 ms 0315: dt=44.800000, rms=0.521 (0.593%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38328.711 ms 0316: dt=27.955654, rms=0.518 (0.591%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38582.078 ms 0317: dt=23.055118, rms=0.516 (0.344%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38583.992 ms 0318: dt=21.454545, rms=0.514 (0.282%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38541.879 ms 0319: dt=21.489051, rms=0.513 (0.214%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38566.586 ms 0320: dt=16.258065, rms=0.512 (0.196%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38555.652 ms 0321: dt=14.222222, rms=0.512 (0.141%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38595.344 ms 0322: dt=32.000000, rms=0.510 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38540.543 ms 0323: dt=16.228571, rms=0.509 (0.213%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38665.508 ms 0324: dt=14.117647, rms=0.509 (0.097%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38736.664 ms 0325: dt=67.254237, rms=0.507 (0.393%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36198.621 ms 0326: dt=12.528302, rms=0.506 (0.178%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38493.852 ms 0327: dt=19.200000, rms=0.505 (0.127%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38710.352 ms 0328: dt=83.428571, rms=0.504 (0.291%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38556.617 ms 0329: dt=27.053140, rms=0.503 (0.239%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38480.953 ms 0330: dt=16.800000, rms=0.502 (0.155%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39928.359 ms 0331: dt=22.441558, rms=0.501 (0.096%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44609.648 ms 0332: dt=11.200000, rms=0.501 (0.048%), neg=0, invalid=766 0333: dt=11.200000, rms=0.501 (0.051%), neg=0, invalid=766 0334: dt=11.200000, rms=0.501 (0.080%), neg=0, invalid=766 0335: dt=11.200000, rms=0.500 (0.121%), neg=0, invalid=766 0336: dt=11.200000, rms=0.499 (0.142%), neg=0, invalid=766 0337: dt=11.200000, rms=0.498 (0.165%), neg=0, invalid=766 0338: dt=11.200000, rms=0.498 (0.176%), neg=0, invalid=766 0339: dt=11.200000, rms=0.497 (0.187%), neg=0, invalid=766 0340: dt=11.200000, rms=0.496 (0.181%), neg=0, invalid=766 0341: dt=11.200000, rms=0.495 (0.175%), neg=0, invalid=766 0342: dt=11.200000, rms=0.494 (0.187%), neg=0, invalid=766 0343: dt=11.200000, rms=0.493 (0.181%), neg=0, invalid=766 0344: dt=11.200000, rms=0.492 (0.166%), neg=0, invalid=766 0345: dt=11.200000, rms=0.491 (0.141%), neg=0, invalid=766 0346: dt=11.200000, rms=0.491 (0.145%), neg=0, invalid=766 0347: dt=11.200000, rms=0.490 (0.154%), neg=0, invalid=766 0348: dt=11.200000, rms=0.489 (0.131%), neg=0, invalid=766 0349: dt=11.200000, rms=0.489 (0.111%), neg=0, invalid=766 0350: dt=11.200000, rms=0.488 (0.099%), neg=0, invalid=766 0351: dt=11.200000, rms=0.488 (0.114%), neg=0, invalid=766 0352: dt=11.200000, rms=0.487 (0.109%), neg=0, invalid=766 0353: dt=11.200000, rms=0.487 (0.088%), neg=0, invalid=766 0354: dt=11.200000, rms=0.487 (0.057%), neg=0, invalid=766 0355: dt=11.200000, rms=0.486 (0.064%), neg=0, invalid=766 0356: dt=11.200000, rms=0.486 (0.075%), neg=0, invalid=766 0357: dt=11.200000, rms=0.486 (0.067%), neg=0, invalid=766 0358: dt=11.200000, rms=0.485 (0.047%), neg=0, invalid=766 0359: dt=11.200000, rms=0.485 (0.048%), neg=0, invalid=766 0360: dt=11.200000, rms=0.485 (0.065%), neg=0, invalid=766 0361: dt=11.200000, rms=0.484 (0.063%), neg=0, invalid=766 0362: dt=11.200000, rms=0.484 (0.042%), neg=0, invalid=766 0363: dt=11.200000, rms=0.484 (0.031%), neg=0, invalid=766 0364: dt=11.200000, rms=0.484 (0.045%), neg=0, invalid=766 0365: dt=11.200000, rms=0.484 (0.051%), neg=0, invalid=766 0366: dt=11.200000, rms=0.483 (0.035%), neg=0, invalid=766 0367: dt=11.200000, rms=0.483 (0.024%), neg=0, invalid=766 0368: dt=11.200000, rms=0.483 (0.030%), neg=0, invalid=766 0369: dt=11.200000, rms=0.483 (0.045%), neg=0, invalid=766 0370: dt=11.200000, rms=0.483 (0.035%), neg=0, invalid=766 0371: dt=11.200000, rms=0.483 (0.023%), neg=0, invalid=766 0372: dt=11.200000, rms=0.483 (0.029%), neg=0, invalid=766 0373: dt=11.200000, rms=0.482 (0.039%), neg=0, invalid=766 0374: dt=11.200000, rms=0.482 (0.033%), neg=0, invalid=766 0375: dt=11.200000, rms=0.482 (0.021%), neg=0, invalid=766 0376: dt=11.200000, rms=0.482 (0.020%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41390.898 ms 0377: dt=44.800000, rms=0.482 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 40661.902 ms 0378: dt=0.000000, rms=0.482 (-0.001%), neg=0, invalid=766 0379: dt=0.250000, rms=0.482 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43674.688 ms 0380: dt=11.840000, rms=0.481 (0.083%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43616.113 ms 0381: dt=32.000000, rms=0.480 (0.211%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 41171.242 ms 0382: dt=2.800000, rms=0.480 (0.012%), neg=0, invalid=766 0383: dt=2.800000, rms=0.480 (0.007%), neg=0, invalid=766 0384: dt=2.800000, rms=0.480 (-0.010%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.511, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36192.012 ms 0385: dt=0.000000, rms=0.511 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36307.113 ms 0386: dt=0.000000, rms=0.511 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.511, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36129.055 ms 0387: dt=0.000000, rms=0.511 (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=0.571, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36110.000 ms 0388: dt=1.844118, rms=0.562 (1.572%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36206.340 ms 0389: dt=1.076190, rms=0.561 (0.184%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36132.828 ms 0390: dt=0.448000, rms=0.561 (0.016%), neg=0, invalid=766 0391: dt=0.448000, rms=0.561 (-0.002%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.561, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36236.156 ms 0392: dt=1.792000, rms=0.559 (0.316%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36042.676 ms 0393: dt=1.024000, rms=0.559 (0.040%), neg=0, invalid=766 0394: dt=1.024000, rms=0.559 (-0.010%), 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=0.517, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36252.730 ms 0395: dt=0.448000, rms=0.504 (2.580%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 38456.809 ms 0396: dt=1.792000, rms=0.492 (2.389%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36114.820 ms 0397: dt=0.096000, rms=0.492 (-0.009%), neg=0, invalid=766 0398: dt=0.096000, rms=0.492 (0.003%), neg=0, invalid=766 0399: dt=0.096000, rms=0.492 (-0.009%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.492, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36013.531 ms 0400: dt=0.448000, rms=0.488 (0.835%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33590.781 ms 0401: dt=0.000000, rms=0.488 (0.002%), neg=0, invalid=766 0402: dt=0.050000, rms=0.488 (-0.003%), 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 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.485, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37598.531 ms 0403: dt=110.976000, rms=0.486 (-0.169%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37740.004 ms 0404: dt=295.936000, rms=0.485 (0.236%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37455.902 ms 0405: dt=110.976000, rms=0.485 (0.101%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 39805.723 ms 0406: dt=92.480000, rms=0.485 (0.026%), neg=0, invalid=766 0407: dt=92.480000, rms=0.484 (0.028%), neg=0, invalid=766 0408: dt=92.480000, rms=0.484 (0.037%), neg=0, invalid=766 0409: dt=92.480000, rms=0.484 (0.050%), neg=0, invalid=766 0410: dt=92.480000, rms=0.484 (0.046%), neg=0, invalid=766 0411: dt=92.480000, rms=0.483 (0.058%), neg=0, invalid=766 0412: dt=92.480000, rms=0.483 (0.051%), neg=0, invalid=766 0413: dt=92.480000, rms=0.483 (0.045%), neg=0, invalid=766 0414: dt=92.480000, rms=0.483 (0.037%), neg=0, invalid=766 0415: dt=92.480000, rms=0.483 (0.034%), neg=0, invalid=766 0416: dt=92.480000, rms=0.482 (0.036%), neg=0, invalid=766 0417: dt=92.480000, rms=0.482 (0.029%), neg=0, invalid=766 0418: dt=92.480000, rms=0.482 (0.027%), neg=0, invalid=766 0419: dt=92.480000, rms=0.482 (0.023%), neg=0, invalid=766 0420: dt=92.480000, rms=0.482 (0.027%), neg=0, invalid=766 0421: dt=92.480000, rms=0.482 (0.027%), neg=0, invalid=766 0422: dt=92.480000, rms=0.482 (0.025%), neg=0, invalid=766 0423: dt=92.480000, rms=0.482 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 46440.961 ms 0424: dt=517.888000, rms=0.482 (0.017%), neg=0, invalid=766 0425: dt=517.888000, rms=0.482 (-0.314%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.482, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 45643.820 ms 0426: dt=31.104000, rms=0.481 (0.090%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42900.258 ms 0427: dt=82.944000, rms=0.481 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 42791.746 ms 0428: dt=145.152000, rms=0.479 (0.389%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 44336.387 ms 0429: dt=16.000000, rms=0.479 (0.005%), neg=0, invalid=766 0430: dt=16.000000, rms=0.479 (0.009%), neg=0, invalid=766 0431: dt=16.000000, rms=0.479 (0.017%), neg=0, invalid=766 0432: dt=16.000000, rms=0.478 (0.030%), neg=0, invalid=766 0433: dt=16.000000, rms=0.478 (0.053%), neg=0, invalid=766 0434: dt=16.000000, rms=0.478 (0.082%), neg=0, invalid=766 0435: dt=16.000000, rms=0.477 (0.098%), neg=0, invalid=766 0436: dt=16.000000, rms=0.477 (0.027%), neg=0, invalid=766 0437: dt=16.000000, rms=0.477 (0.046%), neg=0, invalid=766 0438: dt=16.000000, rms=0.477 (0.016%), neg=0, invalid=766 0439: dt=8.000000, rms=0.477 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32083.080 ms 0440: dt=0.567000, rms=0.477 (0.001%), neg=0, invalid=766 0441: dt=0.141750, rms=0.477 (0.000%), neg=0, invalid=766 0442: dt=0.070875, rms=0.477 (0.000%), neg=0, invalid=766 0443: dt=0.008859, rms=0.477 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34899.473 ms 0444: dt=0.005670, rms=0.477 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 18152.893 ms 0445: dt=0.000000, rms=0.477 (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=0.477, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 17467.143 ms 0446: dt=0.000000, rms=0.477 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.477, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16539.127 ms 0447: dt=0.000000, rms=0.477 (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=0.479, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 16491.928 ms 0448: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 34899.527 ms 0449: dt=4.032000, rms=0.471 (1.654%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32825.906 ms 0450: dt=1.008000, rms=0.470 (0.287%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35317.891 ms 0451: dt=4.032000, rms=0.465 (1.038%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30327.012 ms 0452: dt=1.008000, rms=0.464 (0.195%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30480.301 ms 0453: dt=0.864000, rms=0.463 (0.159%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37672.070 ms 0454: dt=11.520000, rms=0.455 (1.865%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32884.680 ms 0455: dt=1.008000, rms=0.454 (0.076%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30610.314 ms 0456: dt=1.008000, rms=0.454 (0.071%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32835.535 ms 0457: dt=1.008000, rms=0.454 (0.067%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33143.000 ms 0458: dt=1.008000, rms=0.454 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32921.961 ms 0459: dt=1.008000, rms=0.453 (0.061%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35294.965 ms 0460: dt=4.032000, rms=0.452 (0.232%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37713.566 ms 0461: dt=16.128000, rms=0.449 (0.748%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 33017.203 ms 0462: dt=1.008000, rms=0.449 (0.027%), neg=0, invalid=766 0463: dt=1.008000, rms=0.449 (0.028%), neg=0, invalid=766 0464: dt=1.008000, rms=0.448 (0.044%), neg=0, invalid=766 0465: dt=1.008000, rms=0.448 (0.056%), neg=0, invalid=766 0466: dt=1.008000, rms=0.448 (0.066%), neg=0, invalid=766 0467: dt=1.008000, rms=0.447 (0.076%), neg=0, invalid=766 0468: dt=1.008000, rms=0.447 (0.085%), neg=0, invalid=766 0469: dt=1.008000, rms=0.447 (0.093%), neg=0, invalid=766 0470: dt=1.008000, rms=0.446 (0.097%), neg=0, invalid=766 0471: dt=1.008000, rms=0.446 (0.098%), neg=0, invalid=766 0472: dt=1.008000, rms=0.445 (0.093%), neg=0, invalid=766 0473: dt=1.008000, rms=0.445 (0.087%), neg=0, invalid=766 0474: dt=1.008000, rms=0.445 (0.080%), neg=0, invalid=766 0475: dt=1.008000, rms=0.444 (0.074%), neg=0, invalid=766 0476: dt=1.008000, rms=0.444 (0.067%), neg=0, invalid=766 0477: dt=1.008000, rms=0.444 (0.062%), neg=0, invalid=766 0478: dt=1.008000, rms=0.444 (0.054%), neg=0, invalid=766 0479: dt=1.008000, rms=0.443 (0.047%), neg=0, invalid=766 0480: dt=1.008000, rms=0.443 (0.038%), neg=0, invalid=766 0481: dt=1.008000, rms=0.443 (0.032%), neg=0, invalid=766 0482: dt=1.008000, rms=0.443 (0.025%), neg=0, invalid=766 0483: dt=1.008000, rms=0.443 (0.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 37705.723 ms 0484: dt=9.216000, rms=0.443 (0.036%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35304.086 ms 0485: dt=4.032000, rms=0.443 (0.013%), neg=0, invalid=766 0486: dt=4.032000, rms=0.443 (0.005%), neg=0, invalid=766 0487: dt=4.032000, rms=0.443 (0.010%), neg=0, invalid=766 0488: dt=4.032000, rms=0.442 (0.007%), neg=0, invalid=766 0489: dt=4.032000, rms=0.442 (0.004%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.449, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30620.885 ms 0490: dt=0.000000, 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 gcamFindOptimalTimeStep: Complete in 30575.693 ms 0491: dt=0.000000, rms=0.449 (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=0.438, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32922.836 ms 0492: dt=0.133663, rms=0.435 (0.653%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32809.637 ms 0493: dt=0.119924, rms=0.433 (0.423%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32803.750 ms 0494: dt=0.080000, rms=0.433 (0.214%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30593.771 ms 0495: dt=0.028000, rms=0.432 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32911.527 ms 0496: dt=0.112000, rms=0.431 (0.243%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 35345.793 ms 0497: dt=0.320000, rms=0.429 (0.543%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30595.732 ms 0498: dt=0.028000, rms=0.429 (0.022%), neg=0, invalid=766 0499: dt=0.028000, rms=0.429 (0.021%), neg=0, invalid=766 0500: dt=0.028000, rms=0.429 (0.039%), neg=0, invalid=766 0501: dt=0.028000, rms=0.428 (0.054%), neg=0, invalid=766 0502: dt=0.028000, rms=0.428 (0.065%), neg=0, invalid=766 0503: dt=0.028000, rms=0.428 (0.072%), neg=0, invalid=766 0504: dt=0.028000, rms=0.427 (0.076%), neg=0, invalid=766 0505: dt=0.028000, rms=0.427 (0.077%), neg=0, invalid=766 0506: dt=0.028000, rms=0.427 (0.075%), neg=0, invalid=766 0507: dt=0.028000, rms=0.426 (0.071%), neg=0, invalid=766 0508: dt=0.028000, rms=0.426 (0.065%), neg=0, invalid=766 0509: dt=0.028000, rms=0.426 (0.058%), neg=0, invalid=766 0510: dt=0.028000, rms=0.426 (-0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30587.336 ms 0511: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32899.449 ms 0512: dt=0.103205, rms=0.425 (0.210%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30526.428 ms 0513: dt=0.028000, rms=0.425 (0.044%), neg=0, invalid=766 0514: dt=0.028000, rms=0.425 (0.041%), neg=0, invalid=766 0515: dt=0.028000, rms=0.424 (0.075%), neg=0, invalid=766 0516: dt=0.028000, rms=0.424 (0.034%), neg=0, invalid=766 0517: dt=0.028000, rms=0.424 (0.061%), neg=0, invalid=766 0518: dt=0.028000, rms=0.424 (0.081%), neg=0, invalid=766 0519: dt=0.028000, rms=0.423 (0.022%), neg=0, invalid=766 0520: dt=0.028000, rms=0.423 (0.041%), neg=0, invalid=766 0521: dt=0.028000, rms=0.423 (0.019%), neg=0, invalid=766 0522: dt=0.028000, rms=0.423 (0.034%), neg=0, invalid=766 0523: dt=0.028000, rms=0.423 (0.046%), neg=0, invalid=766 0524: dt=0.028000, rms=0.423 (0.053%), neg=0, invalid=766 0525: dt=0.028000, rms=0.422 (0.057%), neg=0, invalid=766 0526: dt=0.028000, rms=0.422 (0.057%), neg=0, invalid=766 0527: dt=0.028000, rms=0.422 (0.054%), neg=0, invalid=766 0528: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 0529: dt=0.028000, rms=0.422 (0.002%), neg=0, invalid=766 0530: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 32835.734 ms 0531: dt=0.080959, rms=0.422 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 30603.018 ms 0532: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 0533: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 0534: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 0535: dt=0.028000, rms=0.422 (0.002%), neg=0, invalid=766 0536: dt=0.028000, rms=0.422 (0.003%), neg=0, invalid=766 0537: dt=0.028000, rms=0.422 (0.004%), neg=0, invalid=766 0538: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 0539: dt=0.028000, rms=0.422 (0.001%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 3 hours, 44 minutes and 9 seconds. #-------------------------------------- #@# CA Reg Inv Wed Aug 17 18:22:50 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed Aug 17 18:24:01 EDT 2011 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 11072325 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 20 seconds. #-------------------------------------- #@# SkullLTA Wed Aug 17 18:25:21 EDT 2011 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /export/data1/tools/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.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.log reading '/export/data1/tools/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=18.0 skull bounding box = (54, 33, 17) --> (208, 206, 223) using (105, 91, 120) as brain centroid... mean wm in atlas = 126, using box (86,70,95) --> (123, 112,145) to find MRI wm before smoothing, mri peak at 164 after smoothing, mri peak at 163, scaling input intensities by 0.773 scaling channel 0 by 0.773006 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10278.2, old_max_log_p =-10412.8 (thresh=-10402.4) 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10278.2, old_max_log_p =-10278.2 (thresh=-10267.9) 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10265.9, old_max_log_p =-10278.2 (thresh=-10267.9) 1.173 -0.078 0.074 -28.111; 0.074 1.122 0.255 -32.672; -0.078 -0.191 0.940 35.029; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10265.4, old_max_log_p =-10265.9 (thresh=-10255.7) 1.171 -0.050 0.114 -35.108; 0.031 1.130 0.318 -36.547; -0.121 -0.261 0.919 48.431; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10262.4, old_max_log_p =-10265.4 (thresh=-10255.2) 1.173 -0.050 0.115 -34.827; 0.031 1.129 0.317 -36.362; -0.121 -0.261 0.920 48.364; 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 1.17251 -0.05002 0.11456 -34.82737; 0.03074 1.12876 0.31740 -36.36204; -0.12084 -0.26133 0.91999 48.36404; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.17251 -0.05002 0.11456 -34.82737; 0.03074 1.12876 0.31740 -36.36204; -0.12084 -0.26133 0.91999 48.36404; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 005: -log(p) = 10262.4 after pass:transform: ( 1.17, -0.05, 0.11, -34.83) ( 0.03, 1.13, 0.32, -36.36) ( -0.12, -0.26, 0.92, 48.36) 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) = 10262.4 tol 0.000010 Resulting transform: 1.173 -0.050 0.115 -34.827; 0.031 1.129 0.317 -36.362; -0.121 -0.261 0.920 48.364; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10262.4 (old=-10412.8) transform before final EM align: 1.173 -0.050 0.115 -34.827; 0.031 1.129 0.317 -36.362; -0.121 -0.261 0.920 48.364; 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 1.17251 -0.05002 0.11456 -34.82737; 0.03074 1.12876 0.31740 -36.36204; -0.12084 -0.26133 0.91999 48.36404; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.17251 -0.05002 0.11456 -34.82737; 0.03074 1.12876 0.31740 -36.36204; -0.12084 -0.26133 0.91999 48.36404; 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) = 1143837.8 tol 0.000000 final transform: 1.173 -0.050 0.115 -34.827; 0.031 1.129 0.317 -36.362; -0.121 -0.261 0.920 48.364; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 25 minutes and 15 seconds. #-------------------------------------- #@# SubCort Seg Wed Aug 17 18:50:36 EDT 2011 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /export/data1/tools/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.07281 (18) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1762 voxels, overlap=0.398) Left_Lateral_Ventricle (4): linear fit = 0.70 x + 0.0 (1762 voxels, peak = 19), gca=18.9 gca peak = 0.14982 (20) mri peak = 0.08747 (19) Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (1601 voxels, overlap=0.535) Right_Lateral_Ventricle (43): linear fit = 0.75 x + 0.0 (1601 voxels, peak = 15), gca=15.0 gca peak = 0.28003 (97) mri peak = 0.08443 (93) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (562 voxels, overlap=0.000) Right_Pallidum (52): linear fit = 0.88 x + 0.0 (562 voxels, peak = 85), gca=84.9 gca peak = 0.18160 (96) mri peak = 0.07227 (85) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (587 voxels, overlap=0.363) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (587 voxels, peak = 84), gca=84.0 gca peak = 0.27536 (62) mri peak = 0.08560 (63) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1044 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1044 voxels, peak = 62), gca=62.0 gca peak = 0.32745 (63) mri peak = 0.07175 (62) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1082 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (1082 voxels, peak = 61), gca=61.4 gca peak = 0.08597 (105) mri peak = 0.07100 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (40798 voxels, overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (40798 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07023 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (39996 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (39996 voxels, peak = 111), gca=111.3 gca peak = 0.07826 (63) mri peak = 0.04135 (62) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (89526 voxels, overlap=0.876) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (89526 voxels, peak = 63), gca=63.0 gca peak = 0.08598 (64) mri peak = 0.03877 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (87410 voxels, overlap=0.904) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (87410 voxels, peak = 64), gca=64.0 gca peak = 0.24164 (71) mri peak = 0.15004 (70) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1393 voxels, overlap=1.000) Right_Caudate (50): linear fit = 0.98 x + 0.0 (1393 voxels, peak = 69), gca=69.2 gca peak = 0.18227 (75) mri peak = 0.13035 (70) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1414 voxels, overlap=0.363) Left_Caudate (11): linear fit = 0.93 x + 0.0 (1414 voxels, peak = 69), gca=69.4 gca peak = 0.10629 (62) mri peak = 0.04643 (63) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (36821 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.08 x + 0.0 (36821 voxels, peak = 67), gca=66.7 gca peak = 0.11668 (59) mri peak = 0.05149 (68) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (38650 voxels, overlap=0.971) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (38650 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.07826 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6187 voxels, overlap=0.912) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (6187 voxels, peak = 92), gca=92.4 gca peak = 0.16819 (86) mri peak = 0.08214 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6551 voxels, overlap=0.972) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (6551 voxels, peak = 88), gca=88.2 gca peak = 0.41688 (64) mri peak = 0.08540 (58) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (581 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 0.93 x + 0.0 (581 voxels, peak = 59), gca=59.2 gca peak = 0.42394 (62) mri peak = 0.08955 (58) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (491 voxels, overlap=0.566) Right_Amygdala (54): linear fit = 0.93 x + 0.0 (491 voxels, peak = 57), gca=57.4 gca peak = 0.10041 (96) mri peak = 0.05987 (82) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (4611 voxels, overlap=0.497) Left_Thalamus_Proper (10): linear fit = 0.90 x + 0.0 (4611 voxels, peak = 86), gca=86.4 gca peak = 0.13978 (88) mri peak = 0.07319 (83) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4601 voxels, overlap=0.757) Right_Thalamus_Proper (49): linear fit = 0.95 x + 0.0 (4601 voxels, peak = 84), gca=83.6 gca peak = 0.08514 (81) mri peak = 0.06559 (76) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2775 voxels, overlap=0.669) Left_Putamen (12): linear fit = 0.93 x + 0.0 (2775 voxels, peak = 75), gca=74.9 gca peak = 0.09624 (82) mri peak = 0.06227 (74) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2719 voxels, overlap=0.625) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2719 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.05484 (90) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12769 voxels, overlap=0.829) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12769 voxels, peak = 90), gca=90.2 gca peak = 0.12757 (95) mri peak = 0.04880 (98) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1766 voxels, overlap=0.856) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (1766 voxels, peak = 97), gca=97.4 gca peak = 0.17004 (92) mri peak = 0.05395 (95) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1856 voxels, overlap=0.977) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (1856 voxels, peak = 90), gca=89.7 gca peak = 0.21361 (36) mri peak = 0.06472 (27) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (77 voxels, overlap=0.209) Third_Ventricle (14): linear fit = 0.82 x + 0.0 (77 voxels, peak = 30), gca=29.7 gca peak = 0.26069 (23) mri peak = 0.08261 (27) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (375 voxels, overlap=0.683) Fourth_Ventricle (15): linear fit = 1.05 x + 0.0 (375 voxels, peak = 24), gca=24.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) 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 0.97 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.83 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.20359 (19) mri peak = 0.07281 (18) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1762 voxels, overlap=0.967) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (1762 voxels, peak = 19), gca=19.5 gca peak = 0.17597 (15) mri peak = 0.08747 (19) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1601 voxels, overlap=0.880) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (1601 voxels, peak = 15), gca=14.6 gca peak = 0.25315 (85) mri peak = 0.08443 (93) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (562 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (562 voxels, peak = 85), gca=85.0 gca peak = 0.18392 (84) mri peak = 0.07227 (85) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (587 voxels, overlap=0.901) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (587 voxels, peak = 84), gca=84.0 gca peak = 0.26320 (62) mri peak = 0.08560 (63) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1044 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1044 voxels, peak = 62), gca=62.0 gca peak = 0.26110 (61) mri peak = 0.07175 (62) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1082 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1082 voxels, peak = 61), gca=61.0 gca peak = 0.08347 (108) mri peak = 0.07100 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40798 voxels, overlap=0.831) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (40798 voxels, peak = 108), gca=108.0 gca peak = 0.08790 (111) mri peak = 0.07023 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39996 voxels, overlap=0.846) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (39996 voxels, peak = 111), gca=111.0 gca peak = 0.07798 (63) mri peak = 0.04135 (62) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (89526 voxels, overlap=0.876) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (89526 voxels, peak = 63), gca=63.0 gca peak = 0.08566 (64) mri peak = 0.03877 (63) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (87410 voxels, overlap=0.904) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (87410 voxels, peak = 64), gca=64.0 gca peak = 0.26772 (69) mri peak = 0.15004 (70) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1393 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1393 voxels, peak = 69), gca=69.0 gca peak = 0.16931 (69) mri peak = 0.13035 (70) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1414 voxels, overlap=0.824) Left_Caudate (11): linear fit = 0.98 x + 0.0 (1414 voxels, peak = 67), gca=67.3 gca peak = 0.09785 (66) mri peak = 0.04643 (63) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36821 voxels, overlap=0.994) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (36821 voxels, peak = 66), gca=66.0 gca peak = 0.12018 (64) mri peak = 0.05149 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (38650 voxels, overlap=0.986) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (38650 voxels, peak = 64), gca=64.0 gca peak = 0.16848 (92) mri peak = 0.07826 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6187 voxels, overlap=0.993) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6187 voxels, peak = 92), gca=92.0 gca peak = 0.14595 (89) mri peak = 0.08214 (88) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6551 voxels, overlap=0.996) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6551 voxels, peak = 89), gca=89.0 gca peak = 0.33075 (59) mri peak = 0.08540 (58) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (581 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (581 voxels, peak = 60), gca=60.5 gca peak = 0.33365 (58) mri peak = 0.08955 (58) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (491 voxels, overlap=0.998) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (491 voxels, peak = 58), gca=58.0 gca peak = 0.10581 (85) mri peak = 0.05987 (82) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4611 voxels, overlap=0.998) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4611 voxels, peak = 85), gca=85.0 gca peak = 0.10689 (81) mri peak = 0.07319 (83) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4601 voxels, overlap=0.944) Right_Thalamus_Proper (49): linear fit = 0.98 x + 0.0 (4601 voxels, peak = 79), gca=79.0 gca peak = 0.10146 (80) mri peak = 0.06559 (76) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2775 voxels, overlap=1.000) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2775 voxels, peak = 80), gca=80.0 gca peak = 0.11778 (70) mri peak = 0.06227 (74) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2719 voxels, overlap=0.929) Right_Putamen (51): linear fit = 0.98 x + 0.0 (2719 voxels, peak = 68), gca=68.2 gca peak = 0.07354 (87) mri peak = 0.05484 (90) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12769 voxels, overlap=0.860) Brain_Stem (16): linear fit = 1.00 x + 0.0 (12769 voxels, peak = 87), gca=87.0 gca peak = 0.14029 (97) mri peak = 0.04880 (98) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1766 voxels, overlap=0.862) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1766 voxels, peak = 97), gca=97.0 gca peak = 0.14816 (90) mri peak = 0.05395 (95) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1856 voxels, overlap=0.950) Left_VentralDC (28): linear fit = 1.02 x + 0.0 (1856 voxels, peak = 92), gca=92.2 gca peak = 0.22645 (31) mri peak = 0.06472 (27) Third_Ventricle (14): linear fit = 0.85 x + 0.0 (77 voxels, overlap=0.656) Third_Ventricle (14): linear fit = 0.85 x + 0.0 (77 voxels, peak = 26), gca=26.4 gca peak = 0.21916 (24) mri peak = 0.08261 (27) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (375 voxels, overlap=0.870) Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (375 voxels, peak = 24), gca=24.0 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26673 (34) gca peak CSF = 0.26405 (32) gca peak Left_Accumbens_area = 0.43216 (65) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.69581 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31193 (32) gca peak Right_Accumbens_area = 0.32727 (70) gca peak Right_vessel = 0.79697 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (35) gca peak WM_hypointensities = 0.13999 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.96 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 15734 gm and wm labels changed (%27 to gray, %73 to white out of all changed labels) 479 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 90909 changed. image ll: -2.179, PF=1.000 pass 2: 16258 changed. image ll: -2.176, PF=1.000 pass 3: 5838 changed. pass 4: 2601 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 19 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/transforms/cc_up.lta NF108_11 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/transforms/cc_up.lta reading aseg from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aseg.auto_noCCseg.mgz reading norm from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/norm.mgz 86858 voxels in left wm, 84388 in right wm, xrange [122, 139] searching rotation angles z=[-3 11], y=[-3 11] searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.9 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.4 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.9 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.4 searching scale 1 Z rot 5.6 searching scale 1 Z rot 5.9 searching scale 1 Z rot 6.1 searching scale 1 Z rot 6.4 searching scale 1 Z rot 6.6 searching scale 1 Z rot 6.9 searching scale 1 Z rot 7.1 searching scale 1 Z rot 7.4 searching scale 1 Z rot 7.6 searching scale 1 Z rot 7.9 searching scale 1 Z rot 8.1 searching scale 1 Z rot 8.4 searching scale 1 Z rot 8.6 searching scale 1 Z rot 8.9 searching scale 1 Z rot 9.1 searching scale 1 Z rot 9.4 searching scale 1 Z rot 9.6 searching scale 1 Z rot 9.9 searching scale 1 Z rot 10.1 searching scale 1 Z rot 10.4 searching scale 1 Z rot 10.6 global minimum found at slice 130.0, rotations (3.81, 3.90) final transformation (x=130.0, yr=3.815, zr=3.899): 0.995 -0.068 0.066 -2.535; 0.068 0.998 0.005 33.906; -0.067 -0.000 0.998 32.879; 0.000 0.000 0.000 1.000; updating x range to be [125, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 152 110 eigenvectors: -0.000 0.007 1.000; -0.160 -0.987 0.007; 0.987 -0.160 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.4 minutes #-------------------------------------- #@# Merge ASeg Wed Aug 17 19:11:13 EDT 2011 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Aug 17 19:11:13 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 1581 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 3 minutes and 28 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 108 gm peak at 64 (64), valley at 23 (23) csf peak at 32, setting threshold to 53 white matter peak found at 111 white matter peak found at 110 gm peak at 64 (64), valley at 23 (23) csf peak at 32, setting threshold to 53 #-------------------------------------------- #@# Mask BFS Wed Aug 17 19:14:43 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1624573 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed Aug 17 19:14:45 EDT 2011 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 (105.0): 105.5 +- 5.8 [80.0 --> 125.0] GM (71.0) : 69.8 +- 9.2 [30.0 --> 96.0] setting bottom of white matter range to 79.0 setting top of gray matter range to 88.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 9699 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6010 filled 6 bright non-wm voxels segmented. 4286 diagonally connected voxels added... white matter segmentation took 1.0 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 0.67 minutes reading wm segmentation from wm.seg.mgz... 729 voxels added to wm to prevent paths from MTL structures to cortex 1464 additional wm voxels added 0 additional wm voxels added SEG EDIT: 52868 voxels turned on, 39995 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+): 27 found - 27 modified | TOTAL: 27 pass 2 (xy+): 0 found - 27 modified | TOTAL: 27 pass 1 (xy-): 26 found - 26 modified | TOTAL: 53 pass 2 (xy-): 0 found - 26 modified | TOTAL: 53 pass 1 (yz+): 27 found - 27 modified | TOTAL: 80 pass 2 (yz+): 0 found - 27 modified | TOTAL: 80 pass 1 (yz-): 22 found - 22 modified | TOTAL: 102 pass 2 (yz-): 0 found - 22 modified | TOTAL: 102 pass 1 (xz+): 24 found - 24 modified | TOTAL: 126 pass 2 (xz+): 0 found - 24 modified | TOTAL: 126 pass 1 (xz-): 25 found - 25 modified | TOTAL: 151 pass 2 (xz-): 0 found - 25 modified | TOTAL: 151 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 16 found - 16 modified | TOTAL: 36 pass 2 (+++): 0 found - 16 modified | TOTAL: 36 pass 1 (+++): 22 found - 22 modified | TOTAL: 58 pass 2 (+++): 0 found - 22 modified | TOTAL: 58 pass 1 (+++): 28 found - 28 modified | TOTAL: 86 pass 2 (+++): 0 found - 28 modified | TOTAL: 86 Iteration Number : 1 pass 1 (++): 201 found - 201 modified | TOTAL: 201 pass 2 (++): 0 found - 201 modified | TOTAL: 201 pass 1 (+-): 190 found - 190 modified | TOTAL: 391 pass 2 (+-): 0 found - 190 modified | TOTAL: 391 pass 1 (--): 161 found - 161 modified | TOTAL: 552 pass 2 (--): 0 found - 161 modified | TOTAL: 552 pass 1 (-+): 202 found - 202 modified | TOTAL: 754 pass 2 (-+): 0 found - 202 modified | TOTAL: 754 Iteration Number : 2 pass 1 (xy+): 5 found - 5 modified | TOTAL: 5 pass 2 (xy+): 0 found - 5 modified | TOTAL: 5 pass 1 (xy-): 8 found - 8 modified | TOTAL: 13 pass 2 (xy-): 0 found - 8 modified | TOTAL: 13 pass 1 (yz+): 4 found - 4 modified | TOTAL: 17 pass 2 (yz+): 0 found - 4 modified | TOTAL: 17 pass 1 (yz-): 8 found - 8 modified | TOTAL: 25 pass 2 (yz-): 0 found - 8 modified | TOTAL: 25 pass 1 (xz+): 5 found - 5 modified | TOTAL: 30 pass 2 (xz+): 0 found - 5 modified | TOTAL: 30 pass 1 (xz-): 5 found - 5 modified | TOTAL: 35 pass 2 (xz-): 0 found - 5 modified | TOTAL: 35 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 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 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 3 found - 3 modified | TOTAL: 5 pass 2 (+-): 0 found - 3 modified | TOTAL: 5 pass 1 (--): 3 found - 3 modified | TOTAL: 8 pass 2 (--): 0 found - 3 modified | TOTAL: 8 pass 1 (-+): 1 found - 1 modified | TOTAL: 9 pass 2 (-+): 0 found - 1 modified | TOTAL: 9 Iteration Number : 3 pass 1 (xy+): 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 (++): 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 (-+): 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 = 1039 (out of 503933: 0.206178) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Aug 17 19:16:27 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2428 (min = 350, max = 1400), aspect = 1.27 (min = 0.10, max = 0.75) need search nearby using seed (126, 113, 89), TAL = (2.0, -39.0, 15.0) talairach voxel to voxel transform 0.846 0.014 -0.078 29.936; -0.039 0.849 -0.276 35.505; 0.062 0.242 0.978 -33.400; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 113, 89) --> (2.0, -39.0, 15.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (2.00, -39.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -39.00, 15.00) SRC: (115.91, 102.69, 87.63) search lh wm seed point around talairach space (-16.00, -39.00, 15.00), SRC: (146.36, 101.29, 89.86) 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 Wed Aug 17 19:17:17 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 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 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 = 8 (out of 241414: 0.003314) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ slice 30: 167 vertices, 201 faces slice 40: 5002 vertices, 5203 faces slice 50: 12852 vertices, 13161 faces slice 60: 22269 vertices, 22638 faces slice 70: 32569 vertices, 33028 faces slice 80: 43690 vertices, 44128 faces slice 90: 54524 vertices, 55004 faces slice 100: 66707 vertices, 67251 faces slice 110: 78609 vertices, 79085 faces slice 120: 90217 vertices, 90753 faces slice 130: 101410 vertices, 101961 faces slice 140: 111919 vertices, 112437 faces slice 150: 121745 vertices, 122213 faces slice 160: 129260 vertices, 129664 faces slice 170: 135571 vertices, 135945 faces slice 180: 140648 vertices, 140964 faces slice 190: 144589 vertices, 144878 faces slice 200: 146050 vertices, 146224 faces slice 210: 146050 vertices, 146224 faces slice 220: 146050 vertices, 146224 faces slice 230: 146050 vertices, 146224 faces slice 240: 146050 vertices, 146224 faces slice 250: 146050 vertices, 146224 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... 146050 voxel in cpt #1: X=-174 [v=146050,e=438672,f=292448] located at (-29.403130, -22.488531, 32.061001) For the whole surface: X=-174 [v=146050,e=438672,f=292448] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed Aug 17 19:17:25 EDT 2011 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 Wed Aug 17 19:17:30 EDT 2011 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts avg radius = 47.9 mm, total surface area = 75316 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.073 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.059 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.052 (target=0.015) step 035: RMS=0.049 (target=0.015) step 040: RMS=0.048 (target=0.015) step 045: RMS=0.047 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.046 (target=0.015) step 060: RMS=0.045 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Aug 17 19:18:28 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.61 (0.00-->6.80) (max @ vno 68502 --> 69833) face area 0.02 +- 0.03 (-0.12-->0.53) scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.598, avgs=0 005/300: dt: 0.9000, rms radial error=177.341, avgs=0 010/300: dt: 0.9000, rms radial error=176.788, avgs=0 015/300: dt: 0.9000, rms radial error=176.060, avgs=0 020/300: dt: 0.9000, rms radial error=175.229, avgs=0 025/300: dt: 0.9000, rms radial error=174.340, avgs=0 030/300: dt: 0.9000, rms radial error=173.418, avgs=0 035/300: dt: 0.9000, rms radial error=172.479, avgs=0 040/300: dt: 0.9000, rms radial error=171.532, avgs=0 045/300: dt: 0.9000, rms radial error=170.582, avgs=0 050/300: dt: 0.9000, rms radial error=169.633, avgs=0 055/300: dt: 0.9000, rms radial error=168.685, avgs=0 060/300: dt: 0.9000, rms radial error=167.741, avgs=0 065/300: dt: 0.9000, rms radial error=166.800, avgs=0 070/300: dt: 0.9000, rms radial error=165.864, avgs=0 075/300: dt: 0.9000, rms radial error=164.932, avgs=0 080/300: dt: 0.9000, rms radial error=164.007, avgs=0 085/300: dt: 0.9000, rms radial error=163.087, avgs=0 090/300: dt: 0.9000, rms radial error=162.171, avgs=0 095/300: dt: 0.9000, rms radial error=161.260, avgs=0 100/300: dt: 0.9000, rms radial error=160.353, avgs=0 105/300: dt: 0.9000, rms radial error=159.452, avgs=0 110/300: dt: 0.9000, rms radial error=158.554, avgs=0 115/300: dt: 0.9000, rms radial error=157.662, avgs=0 120/300: dt: 0.9000, rms radial error=156.774, avgs=0 125/300: dt: 0.9000, rms radial error=155.891, avgs=0 130/300: dt: 0.9000, rms radial error=155.013, avgs=0 135/300: dt: 0.9000, rms radial error=154.139, avgs=0 140/300: dt: 0.9000, rms radial error=153.270, avgs=0 145/300: dt: 0.9000, rms radial error=152.405, avgs=0 150/300: dt: 0.9000, rms radial error=151.545, avgs=0 155/300: dt: 0.9000, rms radial error=150.690, avgs=0 160/300: dt: 0.9000, rms radial error=149.839, avgs=0 165/300: dt: 0.9000, rms radial error=148.993, avgs=0 170/300: dt: 0.9000, rms radial error=148.151, avgs=0 175/300: dt: 0.9000, rms radial error=147.314, avgs=0 180/300: dt: 0.9000, rms radial error=146.481, avgs=0 185/300: dt: 0.9000, rms radial error=145.653, avgs=0 190/300: dt: 0.9000, rms radial error=144.831, avgs=0 195/300: dt: 0.9000, rms radial error=144.014, avgs=0 200/300: dt: 0.9000, rms radial error=143.201, avgs=0 205/300: dt: 0.9000, rms radial error=142.393, avgs=0 210/300: dt: 0.9000, rms radial error=141.589, avgs=0 215/300: dt: 0.9000, rms radial error=140.789, avgs=0 220/300: dt: 0.9000, rms radial error=139.994, avgs=0 225/300: dt: 0.9000, rms radial error=139.204, avgs=0 230/300: dt: 0.9000, rms radial error=138.417, avgs=0 235/300: dt: 0.9000, rms radial error=137.635, avgs=0 240/300: dt: 0.9000, rms radial error=136.858, avgs=0 245/300: dt: 0.9000, rms radial error=136.085, avgs=0 250/300: dt: 0.9000, rms radial error=135.316, avgs=0 255/300: dt: 0.9000, rms radial error=134.552, avgs=0 260/300: dt: 0.9000, rms radial error=133.791, avgs=0 265/300: dt: 0.9000, rms radial error=133.035, avgs=0 270/300: dt: 0.9000, rms radial error=132.283, avgs=0 275/300: dt: 0.9000, rms radial error=131.536, avgs=0 280/300: dt: 0.9000, rms radial error=130.792, avgs=0 285/300: dt: 0.9000, rms radial error=130.053, avgs=0 290/300: dt: 0.9000, rms radial error=129.318, avgs=0 295/300: dt: 0.9000, rms radial error=128.587, avgs=0 300/300: dt: 0.9000, rms radial error=127.860, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 7729.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 2 (K=80.0), pass 1, starting sse = 1163.01 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00056 epoch 3 (K=320.0), pass 1, starting sse = 129.39 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00706 epoch 4 (K=1280.0), pass 1, starting sse = 15.59 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00644 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.09 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed Aug 17 19:24:09 EDT 2011 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 NF108_11 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 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-174 (nv=146050, nf=292448, ne=438672, g=88) 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... 16047 ambiguous faces found in tessellation segmenting defects... 105 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 61 into 54 -merging segment 80 into 74 -merging segment 85 into 74 -merging segment 104 into 103 101 defects to be corrected 0 vertices coincident reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4519 (-4.7259) -vertex loglikelihood: -6.3552 (-3.1776) -normal dot loglikelihood: -3.5217 (-3.5217) -quad curv loglikelihood: -6.5381 (-3.2690) Total Loglikelihood : -25.8668 CORRECTING DEFECT 0 (vertices=1159, convex hull=487) After retessellation of defect 0, euler #=-100 (136637,406807,270070) : difference with theory (-98) = 2 CORRECTING DEFECT 1 (vertices=17, convex hull=54) After retessellation of defect 1, euler #=-99 (136645,406851,270107) : difference with theory (-97) = 2 CORRECTING DEFECT 2 (vertices=58, convex hull=48) After retessellation of defect 2, euler #=-98 (136656,406901,270147) : difference with theory (-96) = 2 CORRECTING DEFECT 3 (vertices=8, convex hull=23) After retessellation of defect 3, euler #=-97 (136657,406910,270156) : difference with theory (-95) = 2 CORRECTING DEFECT 4 (vertices=43, convex hull=89) After retessellation of defect 4, euler #=-96 (136675,406999,270228) : difference with theory (-94) = 2 CORRECTING DEFECT 5 (vertices=41, convex hull=79) After retessellation of defect 5, euler #=-95 (136689,407075,270291) : difference with theory (-93) = 2 CORRECTING DEFECT 6 (vertices=29, convex hull=44) After retessellation of defect 6, euler #=-94 (136699,407119,270326) : difference with theory (-92) = 2 CORRECTING DEFECT 7 (vertices=42, convex hull=32) After retessellation of defect 7, euler #=-93 (136702,407142,270347) : difference with theory (-91) = 2 CORRECTING DEFECT 8 (vertices=229, convex hull=143) After retessellation of defect 8, euler #=-92 (136757,407374,270525) : difference with theory (-90) = 2 CORRECTING DEFECT 9 (vertices=72, convex hull=73) After retessellation of defect 9, euler #=-91 (136773,407451,270587) : difference with theory (-89) = 2 CORRECTING DEFECT 10 (vertices=202, convex hull=186) After retessellation of defect 10, euler #=-90 (136842,407749,270817) : difference with theory (-88) = 2 CORRECTING DEFECT 11 (vertices=25, convex hull=25) After retessellation of defect 11, euler #=-89 (136843,407761,270829) : difference with theory (-87) = 2 CORRECTING DEFECT 12 (vertices=197, convex hull=133) After retessellation of defect 12, euler #=-88 (136899,407993,271006) : difference with theory (-86) = 2 CORRECTING DEFECT 13 (vertices=102, convex hull=66) After retessellation of defect 13, euler #=-87 (136916,408068,271065) : difference with theory (-85) = 2 CORRECTING DEFECT 14 (vertices=56, convex hull=46) After retessellation of defect 14, euler #=-86 (136925,408113,271102) : difference with theory (-84) = 2 CORRECTING DEFECT 15 (vertices=39, convex hull=55) After retessellation of defect 15, euler #=-85 (136933,408161,271143) : difference with theory (-83) = 2 CORRECTING DEFECT 16 (vertices=43, convex hull=71) After retessellation of defect 16, euler #=-84 (136957,408267,271226) : difference with theory (-82) = 2 CORRECTING DEFECT 17 (vertices=22, convex hull=25) After retessellation of defect 17, euler #=-83 (136959,408284,271242) : difference with theory (-81) = 2 CORRECTING DEFECT 18 (vertices=42, convex hull=81) After retessellation of defect 18, euler #=-82 (136970,408348,271296) : difference with theory (-80) = 2 CORRECTING DEFECT 19 (vertices=49, convex hull=55) After retessellation of defect 19, euler #=-81 (136979,408396,271336) : difference with theory (-79) = 2 CORRECTING DEFECT 20 (vertices=53, convex hull=70) After retessellation of defect 20, euler #=-80 (136988,408451,271383) : difference with theory (-78) = 2 CORRECTING DEFECT 21 (vertices=116, convex hull=99) After retessellation of defect 21, euler #=-79 (137017,408584,271488) : difference with theory (-77) = 2 CORRECTING DEFECT 22 (vertices=7, convex hull=28) After retessellation of defect 22, euler #=-78 (137018,408594,271498) : difference with theory (-76) = 2 CORRECTING DEFECT 23 (vertices=545, convex hull=139) After retessellation of defect 23, euler #=-78 (137063,408796,271655) : difference with theory (-75) = 3 CORRECTING DEFECT 24 (vertices=32, convex hull=30) After retessellation of defect 24, euler #=-77 (137066,408814,271671) : difference with theory (-74) = 3 CORRECTING DEFECT 25 (vertices=33, convex hull=97) After retessellation of defect 25, euler #=-76 (137084,408908,271748) : difference with theory (-73) = 3 CORRECTING DEFECT 26 (vertices=21, convex hull=21) After retessellation of defect 26, euler #=-75 (137086,408921,271760) : difference with theory (-72) = 3 CORRECTING DEFECT 27 (vertices=138, convex hull=103) After retessellation of defect 27, euler #=-74 (137126,409088,271888) : difference with theory (-71) = 3 CORRECTING DEFECT 28 (vertices=76, convex hull=69) After retessellation of defect 28, euler #=-73 (137145,409175,271957) : difference with theory (-70) = 3 CORRECTING DEFECT 29 (vertices=169, convex hull=158) After retessellation of defect 29, euler #=-72 (137195,409399,272132) : difference with theory (-69) = 3 CORRECTING DEFECT 30 (vertices=132, convex hull=76) After retessellation of defect 30, euler #=-71 (137207,409462,272184) : difference with theory (-68) = 3 CORRECTING DEFECT 31 (vertices=18, convex hull=35) After retessellation of defect 31, euler #=-70 (137208,409476,272198) : difference with theory (-67) = 3 CORRECTING DEFECT 32 (vertices=100, convex hull=126) After retessellation of defect 32, euler #=-69 (137257,409681,272355) : difference with theory (-66) = 3 CORRECTING DEFECT 33 (vertices=16, convex hull=36) After retessellation of defect 33, euler #=-68 (137264,409712,272380) : difference with theory (-65) = 3 CORRECTING DEFECT 34 (vertices=28, convex hull=66) After retessellation of defect 34, euler #=-67 (137281,409787,272439) : difference with theory (-64) = 3 CORRECTING DEFECT 35 (vertices=20, convex hull=25) After retessellation of defect 35, euler #=-66 (137282,409801,272453) : difference with theory (-63) = 3 CORRECTING DEFECT 36 (vertices=128, convex hull=185) After retessellation of defect 36, euler #=-65 (137341,410059,272653) : difference with theory (-62) = 3 CORRECTING DEFECT 37 (vertices=54, convex hull=93) After retessellation of defect 37, euler #=-64 (137367,410178,272747) : difference with theory (-61) = 3 CORRECTING DEFECT 38 (vertices=7, convex hull=17) After retessellation of defect 38, euler #=-63 (137367,410179,272749) : difference with theory (-60) = 3 CORRECTING DEFECT 39 (vertices=58, convex hull=66) After retessellation of defect 39, euler #=-62 (137403,410315,272850) : difference with theory (-59) = 3 CORRECTING DEFECT 40 (vertices=33, convex hull=61) After retessellation of defect 40, euler #=-61 (137421,410392,272910) : difference with theory (-58) = 3 CORRECTING DEFECT 41 (vertices=116, convex hull=93) After retessellation of defect 41, euler #=-60 (137454,410530,273016) : difference with theory (-57) = 3 CORRECTING DEFECT 42 (vertices=25, convex hull=48) After retessellation of defect 42, euler #=-59 (137465,410581,273057) : difference with theory (-56) = 3 CORRECTING DEFECT 43 (vertices=57, convex hull=93) After retessellation of defect 43, euler #=-58 (137492,410700,273150) : difference with theory (-55) = 3 CORRECTING DEFECT 44 (vertices=77, convex hull=118) After retessellation of defect 44, euler #=-57 (137525,410853,273271) : difference with theory (-54) = 3 CORRECTING DEFECT 45 (vertices=31, convex hull=31) After retessellation of defect 45, euler #=-56 (137529,410874,273289) : difference with theory (-53) = 3 CORRECTING DEFECT 46 (vertices=27, convex hull=74) After retessellation of defect 46, euler #=-55 (137543,410944,273346) : difference with theory (-52) = 3 CORRECTING DEFECT 47 (vertices=31, convex hull=85) After retessellation of defect 47, euler #=-54 (137564,411041,273423) : difference with theory (-51) = 3 CORRECTING DEFECT 48 (vertices=28, convex hull=41) After retessellation of defect 48, euler #=-53 (137573,411081,273455) : difference with theory (-50) = 3 CORRECTING DEFECT 49 (vertices=35, convex hull=55) After retessellation of defect 49, euler #=-52 (137587,411144,273505) : difference with theory (-49) = 3 CORRECTING DEFECT 50 (vertices=29, convex hull=72) After retessellation of defect 50, euler #=-51 (137600,411211,273560) : difference with theory (-48) = 3 CORRECTING DEFECT 51 (vertices=294, convex hull=78) After retessellation of defect 51, euler #=-50 (137628,411328,273650) : difference with theory (-47) = 3 CORRECTING DEFECT 52 (vertices=48, convex hull=83) After retessellation of defect 52, euler #=-49 (137655,411438,273734) : difference with theory (-46) = 3 CORRECTING DEFECT 53 (vertices=13, convex hull=22) After retessellation of defect 53, euler #=-48 (137656,411449,273745) : difference with theory (-45) = 3 CORRECTING DEFECT 54 (vertices=312, convex hull=139) After retessellation of defect 54, euler #=-47 (137746,411801,274008) : difference with theory (-44) = 3 CORRECTING DEFECT 55 (vertices=75, convex hull=111) After retessellation of defect 55, euler #=-46 (137782,411955,274127) : difference with theory (-43) = 3 CORRECTING DEFECT 56 (vertices=9, convex hull=23) After retessellation of defect 56, euler #=-45 (137783,411965,274137) : difference with theory (-42) = 3 CORRECTING DEFECT 57 (vertices=38, convex hull=28) After retessellation of defect 57, euler #=-44 (137785,411987,274158) : difference with theory (-41) = 3 CORRECTING DEFECT 58 (vertices=57, convex hull=85) After retessellation of defect 58, euler #=-43 (137805,412085,274237) : difference with theory (-40) = 3 CORRECTING DEFECT 59 (vertices=21, convex hull=26) After retessellation of defect 59, euler #=-42 (137808,412101,274251) : difference with theory (-39) = 3 CORRECTING DEFECT 60 (vertices=18, convex hull=58) After retessellation of defect 60, euler #=-41 (137819,412156,274296) : difference with theory (-38) = 3 CORRECTING DEFECT 61 (vertices=22, convex hull=28) After retessellation of defect 61, euler #=-40 (137820,412170,274310) : difference with theory (-37) = 3 CORRECTING DEFECT 62 (vertices=18, convex hull=28) After retessellation of defect 62, euler #=-39 (137822,412183,274322) : difference with theory (-36) = 3 CORRECTING DEFECT 63 (vertices=27, convex hull=59) After retessellation of defect 63, euler #=-38 (137838,412254,274378) : difference with theory (-35) = 3 CORRECTING DEFECT 64 (vertices=499, convex hull=212) After retessellation of defect 64, euler #=-37 (137884,412504,274583) : difference with theory (-34) = 3 CORRECTING DEFECT 65 (vertices=23, convex hull=41) After retessellation of defect 65, euler #=-36 (137898,412561,274627) : difference with theory (-33) = 3 CORRECTING DEFECT 66 (vertices=57, convex hull=75) After retessellation of defect 66, euler #=-35 (137928,412683,274720) : difference with theory (-32) = 3 CORRECTING DEFECT 67 (vertices=27, convex hull=52) After retessellation of defect 67, euler #=-34 (137939,412737,274764) : difference with theory (-31) = 3 CORRECTING DEFECT 68 (vertices=57, convex hull=62) After retessellation of defect 68, euler #=-33 (137961,412828,274834) : difference with theory (-30) = 3 CORRECTING DEFECT 69 (vertices=450, convex hull=263) After retessellation of defect 69, euler #=-32 (138107,413394,275255) : difference with theory (-29) = 3 CORRECTING DEFECT 70 (vertices=76, convex hull=66) After retessellation of defect 70, euler #=-31 (138125,413476,275320) : difference with theory (-28) = 3 CORRECTING DEFECT 71 (vertices=291, convex hull=105) After retessellation of defect 71, euler #=-30 (138163,413643,275450) : difference with theory (-27) = 3 CORRECTING DEFECT 72 (vertices=58, convex hull=34) After retessellation of defect 72, euler #=-29 (138171,413681,275481) : difference with theory (-26) = 3 CORRECTING DEFECT 73 (vertices=670, convex hull=236) After retessellation of defect 73, euler #=-26 (138259,414064,275779) : difference with theory (-25) = 1 CORRECTING DEFECT 74 (vertices=65, convex hull=122) After retessellation of defect 74, euler #=-25 (138292,414216,275899) : difference with theory (-24) = 1 CORRECTING DEFECT 75 (vertices=40, convex hull=51) After retessellation of defect 75, euler #=-24 (138311,414296,275961) : difference with theory (-23) = 1 CORRECTING DEFECT 76 (vertices=38, convex hull=50) After retessellation of defect 76, euler #=-23 (138314,414322,275985) : difference with theory (-22) = 1 CORRECTING DEFECT 77 (vertices=22, convex hull=56) After retessellation of defect 77, euler #=-22 (138326,414378,276030) : difference with theory (-21) = 1 CORRECTING DEFECT 78 (vertices=32, convex hull=77) After retessellation of defect 78, euler #=-21 (138335,414437,276081) : difference with theory (-20) = 1 CORRECTING DEFECT 79 (vertices=42, convex hull=37) After retessellation of defect 79, euler #=-20 (138344,414480,276116) : difference with theory (-19) = 1 CORRECTING DEFECT 80 (vertices=31, convex hull=67) After retessellation of defect 80, euler #=-19 (138358,414550,276173) : difference with theory (-18) = 1 CORRECTING DEFECT 81 (vertices=30, convex hull=72) After retessellation of defect 81, euler #=-18 (138371,414613,276224) : difference with theory (-17) = 1 CORRECTING DEFECT 82 (vertices=19, convex hull=29) After retessellation of defect 82, euler #=-17 (138374,414630,276239) : difference with theory (-16) = 1 CORRECTING DEFECT 83 (vertices=56, convex hull=69) After retessellation of defect 83, euler #=-16 (138398,414728,276314) : difference with theory (-15) = 1 CORRECTING DEFECT 84 (vertices=169, convex hull=102) After retessellation of defect 84, euler #=-15 (138414,414823,276394) : difference with theory (-14) = 1 CORRECTING DEFECT 85 (vertices=55, convex hull=45) After retessellation of defect 85, euler #=-14 (138426,414877,276437) : difference with theory (-13) = 1 CORRECTING DEFECT 86 (vertices=102, convex hull=91) After retessellation of defect 86, euler #=-13 (138463,415034,276558) : difference with theory (-12) = 1 CORRECTING DEFECT 87 (vertices=28, convex hull=17) After retessellation of defect 87, euler #=-12 (138466,415047,276569) : difference with theory (-11) = 1 CORRECTING DEFECT 88 (vertices=21, convex hull=61) After retessellation of defect 88, euler #=-11 (138477,415104,276616) : difference with theory (-10) = 1 CORRECTING DEFECT 89 (vertices=8, convex hull=33) After retessellation of defect 89, euler #=-10 (138478,415116,276628) : difference with theory (-9) = 1 CORRECTING DEFECT 90 (vertices=20, convex hull=23) After retessellation of defect 90, euler #=-9 (138480,415132,276643) : difference with theory (-8) = 1 CORRECTING DEFECT 91 (vertices=26, convex hull=38) After retessellation of defect 91, euler #=-8 (138482,415149,276659) : difference with theory (-7) = 1 CORRECTING DEFECT 92 (vertices=105, convex hull=43) After retessellation of defect 92, euler #=-7 (138490,415185,276688) : difference with theory (-6) = 1 CORRECTING DEFECT 93 (vertices=33, convex hull=46) After retessellation of defect 93, euler #=-6 (138499,415230,276725) : difference with theory (-5) = 1 CORRECTING DEFECT 94 (vertices=12, convex hull=25) After retessellation of defect 94, euler #=-5 (138499,415241,276737) : difference with theory (-4) = 1 CORRECTING DEFECT 95 (vertices=28, convex hull=53) After retessellation of defect 95, euler #=-4 (138507,415288,276777) : difference with theory (-3) = 1 CORRECTING DEFECT 96 (vertices=126, convex hull=118) After retessellation of defect 96, euler #=-3 (138531,415412,276878) : difference with theory (-2) = 1 CORRECTING DEFECT 97 (vertices=60, convex hull=94) After retessellation of defect 97, euler #=-2 (138558,415538,276978) : difference with theory (-1) = 1 CORRECTING DEFECT 98 (vertices=167, convex hull=65) After retessellation of defect 98, euler #=-1 (138565,415586,277020) : difference with theory (0) = 1 CORRECTING DEFECT 99 (vertices=77, convex hull=33) After retessellation of defect 99, euler #=0 (138571,415611,277040) : difference with theory (1) = 1 CORRECTING DEFECT 100 (vertices=280, convex hull=184) After retessellation of defect 100, euler #=2 (138624,415866,277244) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.04-->11.24) (max @ vno 18604 --> 27678) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.04-->11.24) (max @ vno 18604 --> 27678) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 323 mutations (34.7%), 608 crossovers (65.3%), 417 vertices were eliminated building final representation... 7426 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=138624, nf=277244, ne=415866, g=0) writing corrected surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 74.9 minutes 0 defective edges removing intersecting faces 000: 783 intersecting 001: 29 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 138624 - 415866 + 277244 = 2 --> 0 holes F =2V-4: 277244 = 277248-4 (0) 2E=3F: 831732 = 831732 (0) total defect index = 0 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 117 intersecting 001: 4 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make Final Surf lh Wed Aug 17 20:39:09 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs NF108_11 lh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/filled.mgz... reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/brain.finalsurfs.mgz... reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... 24438 bright wm thresholded. 10 bright non-wm voxels segmented. reading original surface position from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.orig... computing class statistics... border white: 252840 voxels (1.51%) border gray 310905 voxels (1.85%) WM (96.0): 96.8 +- 8.8 [70.0 --> 110.0] GM (71.0) : 70.4 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 58.2 (was 70) setting MAX_BORDER_WHITE to 110.8 (was 105) setting MIN_BORDER_WHITE to 68.0 (was 85) setting MAX_CSF to 48.4 (was 40) setting MAX_GRAY to 93.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 63.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 38.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.24 (0.02-->4.62) (max @ vno 137977 --> 138014) face area 0.28 +- 0.13 (0.00-->5.67) mean absolute distance = 0.61 +- 0.73 3491 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=68 using class modes intead of means.... mean inside = 92.6, mean outside = 74.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=79.3, 143 (143) missing vertices, mean dist 0.3 [0.5 (%36.2)->0.7 (%63.8))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.07-->4.85) (max @ vno 137977 --> 138014) face area 0.28 +- 0.14 (0.00-->5.07) mean absolute distance = 0.31 +- 0.50 2923 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5131075.5, rms=9.35 001: dt: 0.5000, sse=6348730.5, rms=6.59 002: dt: 0.5000, sse=7078782.5, rms=5.31 003: dt: 0.5000, sse=7496818.5, rms=4.69 004: dt: 0.5000, sse=7797914.5, rms=4.29 005: dt: 0.5000, sse=7856522.0, rms=4.10 006: dt: 0.5000, sse=8031020.0, rms=3.91 007: dt: 0.5000, sse=8019293.5, rms=3.86 008: dt: 0.5000, sse=8088276.0, rms=3.76 rms = 3.75, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8034798.5, rms=3.75 010: dt: 0.2500, sse=5322187.0, rms=2.71 011: dt: 0.2500, sse=4929972.0, rms=2.44 012: dt: 0.2500, sse=4717449.5, rms=2.37 rms = 2.33, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4663190.0, rms=2.33 014: dt: 0.1250, sse=4558757.5, rms=2.27 rms = 2.26, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=4529405.0, rms=2.26 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.1, 199 (24) missing vertices, mean dist -0.1 [0.3 (%71.6)->0.3 (%28.4))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.27 (0.07-->4.84) (max @ vno 137977 --> 138014) face area 0.34 +- 0.17 (0.00-->6.52) mean absolute distance = 0.25 +- 0.40 2873 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4957298.0, rms=4.10 016: dt: 0.5000, sse=5639260.5, rms=2.90 rms = 3.26, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=5241761.5, rms=2.20 018: dt: 0.2500, sse=5088054.0, rms=1.91 019: dt: 0.2500, sse=5006629.5, rms=1.81 rms = 1.80, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=4962133.0, rms=1.80 rms = 1.76, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=4901411.5, rms=1.76 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=83.8, 184 (18) missing vertices, mean dist -0.1 [0.3 (%63.3)->0.2 (%36.7))] %87 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.07-->4.71) (max @ vno 137977 --> 138014) face area 0.34 +- 0.17 (0.00-->6.70) mean absolute distance = 0.24 +- 0.36 3035 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4992632.5, rms=2.62 rms = 2.74, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=4972240.5, rms=1.99 023: dt: 0.2500, sse=5030441.0, rms=1.65 rms = 1.62, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=5104510.0, rms=1.62 rms = 1.57, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5032582.5, rms=1.57 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=84.4, 182 (15) missing vertices, mean dist -0.0 [0.2 (%53.2)->0.2 (%46.8))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5041591.0, rms=1.72 rms = 1.87, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5191678.0, rms=1.36 027: dt: 0.2500, sse=5512186.0, rms=1.20 rms = 1.21, time step reduction 2 of 3 to 0.125... rms = 1.20, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=5515620.0, rms=1.20 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 3 vertex label from ripped group correcting aseg with surfaces... label Left_Hippocampus: removing 4 voxels in segment 0 label Left_Hippocampus: removing 474 voxels in segment 1 label Left_Hippocampus: removing 238 voxels in segment 2 label Left_Hippocampus: removing 65 voxels in segment 3 label Left_Hippocampus: removing 1 voxels in segment 5 label Left_Hippocampus: removing 28 voxels in segment 6 label Right_Hippocampus: removing 16 voxels in segment 1 label Left_Amygdala: removing 10 voxels in segment 1 label Left_Amygdala: removing 7 voxels in segment 2 label Left_Amygdala: removing 1 voxels in segment 3 label Left_Amygdala: removing 1 voxels in segment 4 generating cortex label... 15 non-cortical segments detected only using segment with 1797 vertices erasing segment 1 (vno[0] = 66231) erasing segment 2 (vno[0] = 75227) erasing segment 3 (vno[0] = 78607) erasing segment 4 (vno[0] = 80909) erasing segment 5 (vno[0] = 82749) erasing segment 6 (vno[0] = 87227) erasing segment 7 (vno[0] = 95023) erasing segment 8 (vno[0] = 95735) erasing segment 9 (vno[0] = 96810) erasing segment 10 (vno[0] = 97973) erasing segment 11 (vno[0] = 99006) erasing segment 12 (vno[0] = 104407) erasing segment 13 (vno[0] = 106350) erasing segment 14 (vno[0] = 106375) writing cortex label to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/label/lh.cortex.label... LabelWrite: saving to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/label/lh.cortex.label writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.curv writing smoothed area to lh.area writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.area vertex spacing 0.90 +- 0.27 (0.05-->4.73) (max @ vno 137977 --> 138014) face area 0.34 +- 0.17 (0.00-->6.64) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=59.2, 161 (161) missing vertices, mean dist 1.8 [0.0 (%0.0)->2.9 (%100.0))] %16 local maxima, %44 large gradients and %37 min vals, 4051 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=20104404.0, rms=25.27 001: dt: 0.5000, sse=15115717.0, rms=21.20 002: dt: 0.5000, sse=11691925.0, rms=17.89 003: dt: 0.5000, sse=9516650.0, rms=15.27 004: dt: 0.5000, sse=8284817.0, rms=13.22 005: dt: 0.5000, sse=7599973.5, rms=11.63 006: dt: 0.5000, sse=7171687.0, rms=10.42 007: dt: 0.5000, sse=6921736.0, rms=9.46 008: dt: 0.5000, sse=6767871.5, rms=8.70 009: dt: 0.5000, sse=6776187.0, rms=8.10 010: dt: 0.5000, sse=6796859.5, rms=7.60 011: dt: 0.5000, sse=6920962.0, rms=7.17 012: dt: 0.5000, sse=7029371.5, rms=6.77 013: dt: 0.5000, sse=7152825.0, rms=6.45 014: dt: 0.5000, sse=7325568.0, rms=6.15 015: dt: 0.5000, sse=7449741.5, rms=5.88 016: dt: 0.5000, sse=7558969.5, rms=5.62 017: dt: 0.5000, sse=7674742.0, rms=5.39 018: dt: 0.5000, sse=7770245.5, rms=5.17 019: dt: 0.5000, sse=7842836.0, rms=5.00 020: dt: 0.5000, sse=7877016.0, rms=4.87 021: dt: 0.5000, sse=7954952.0, rms=4.78 022: dt: 0.5000, sse=7972393.0, rms=4.71 023: dt: 0.5000, sse=8019276.0, rms=4.64 024: dt: 0.5000, sse=8014258.5, rms=4.59 rms = 4.54, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=8058660.0, rms=4.54 026: dt: 0.2500, sse=6879216.5, rms=4.34 027: dt: 0.2500, sse=6776937.5, rms=4.28 rms = 4.27, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=6711364.0, rms=4.27 rms = 4.22, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=6540435.0, rms=4.22 positioning took 3.1 minutes mean border=57.6, 1755 (38) missing vertices, mean dist 0.3 [0.3 (%43.3)->1.1 (%56.7))] %34 local maxima, %30 large gradients and %31 min vals, 2160 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7210357.5, rms=5.52 030: dt: 0.5000, sse=7350681.0, rms=5.10 031: dt: 0.5000, sse=8486287.0, rms=4.87 032: dt: 0.5000, sse=8387908.5, rms=4.75 033: dt: 0.5000, sse=9101626.0, rms=4.63 034: dt: 0.5000, sse=8892923.0, rms=4.55 035: dt: 0.5000, sse=9355047.0, rms=4.45 036: dt: 0.5000, sse=9091196.0, rms=4.40 037: dt: 0.5000, sse=9478992.0, rms=4.34 rms = 4.31, time step reduction 1 of 3 to 0.250... 038: dt: 0.5000, sse=9187785.0, rms=4.31 039: dt: 0.2500, sse=8062313.0, rms=4.03 040: dt: 0.2500, sse=7970055.0, rms=3.94 rms = 3.95, time step reduction 2 of 3 to 0.125... rms = 3.92, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=7894550.5, rms=3.92 positioning took 1.4 minutes mean border=56.7, 2494 (24) missing vertices, mean dist 0.2 [0.3 (%40.7)->0.7 (%59.3))] %46 local maxima, %18 large gradients and %30 min vals, 2371 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8020923.0, rms=4.22 rms = 4.29, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=7775210.5, rms=4.06 043: dt: 0.2500, sse=7682077.5, rms=3.96 rms = 3.93, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=7823943.5, rms=3.93 045: dt: 0.1250, sse=7681917.0, rms=3.85 rms = 3.82, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=7734001.0, rms=3.82 positioning took 0.6 minutes mean border=56.2, 4855 (21) missing vertices, mean dist 0.1 [0.3 (%42.8)->0.5 (%57.2))] %49 local maxima, %14 large gradients and %30 min vals, 2265 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=7738558.0, rms=3.86 rms = 3.90, time step reduction 1 of 3 to 0.250... 047: dt: 0.2500, sse=7730245.0, rms=3.77 048: dt: 0.2500, sse=8072376.5, rms=3.69 rms = 3.65, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=8270567.5, rms=3.65 050: dt: 0.1250, sse=8190277.0, rms=3.57 rms = 3.54, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=8262108.5, rms=3.54 positioning took 0.6 minutes writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.area.pial vertex spacing 1.08 +- 0.50 (0.04-->8.54) (max @ vno 92646 --> 91634) face area 0.46 +- 0.39 (0.00-->8.32) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 138624 vertices processed 25000 of 138624 vertices processed 50000 of 138624 vertices processed 75000 of 138624 vertices processed 100000 of 138624 vertices processed 125000 of 138624 vertices processed 0 of 138624 vertices processed 25000 of 138624 vertices processed 50000 of 138624 vertices processed 75000 of 138624 vertices processed 100000 of 138624 vertices processed 125000 of 138624 vertices processed thickness calculation complete, 5030:5514 truncations. 39178 vertices at 0 distance 61610 vertices at 1 distance 72440 vertices at 2 distance 50497 vertices at 3 distance 24224 vertices at 4 distance 9788 vertices at 5 distance 4062 vertices at 6 distance 1864 vertices at 7 distance 1029 vertices at 8 distance 598 vertices at 9 distance 380 vertices at 10 distance 288 vertices at 11 distance 178 vertices at 12 distance 140 vertices at 13 distance 122 vertices at 14 distance 106 vertices at 15 distance 80 vertices at 16 distance 62 vertices at 17 distance 60 vertices at 18 distance 62 vertices at 19 distance 120 vertices at 20 distance writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.thickness positioning took 14.6 minutes #-------------------------------------------- #@# Surf Volume lh Wed Aug 17 20:53:43 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness #-------------------------------------------- #@# Smooth2 lh Wed Aug 17 20:53:43 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 Wed Aug 17 20:53:47 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.6 mm, total surface area = 85161 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.070 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.050 (target=0.015) step 025: RMS=0.042 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.019 (target=0.015) inflation complete. inflation took 0.9 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 312 vertices thresholded to be in k1 ~ [-0.36 0.32], k2 ~ [-0.14 0.10] total integrated curvature = 0.296*4pi (3.718) --> 1 handles ICI = 1.4, FI = 10.7, variation=175.983 191 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 159 vertices thresholded to be in [-0.19 0.13] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.018, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Wed Aug 17 20:56:10 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm NF108_11 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 [ NF108_11/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 301 ] WARN: S lookup min: -1.227762 WARN: S explicit min: 0.000000 vertex = 158 #-------------------------------------------- #@# Sphere lh Wed Aug 17 20:56:15 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.62 hours scaling brain by 0.275... pass 1: epoch 1 of 3 starting distance error %22.37 pass 1: epoch 2 of 3 starting distance error %22.26 unfolding complete - removing small folds... starting distance error %21.80 removing remaining folds... final distance error %21.81 429: 0 negative triangles #-------------------------------------------- #@# Surf Reg lh Wed Aug 17 22:33:32 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_register -curv ../surf/lh.sphere /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.598 curvature mean = 0.013, std = 0.930 curvature mean = 0.022, std = 0.862 curvature mean = -0.014, std = 0.950 curvature mean = 0.010, std = 0.940 curvature mean = -0.015, std = 0.962 curvature mean = 0.004, std = 0.973 curvature mean = -0.018, std = 0.964 curvature mean = 0.001, std = 0.988 curvature mean = -0.044, std = 0.387 curvature mean = 0.001, std = 0.067 curvature mean = 0.079, std = 0.258 curvature mean = 0.000, std = 0.080 curvature mean = 0.059, std = 0.398 curvature mean = 0.001, std = 0.086 curvature mean = 0.036, std = 0.524 curvature mean = 0.001, std = 0.088 curvature mean = 0.013, std = 0.648 216: 0 negative triangles #-------------------------------------------- #@# Jacobian white lh Wed Aug 17 23:29:26 EDT 2011 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 Wed Aug 17 23:29:28 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mrisp_paint -a 5 /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Wed Aug 17 23:29:30 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 lh ../surf/lh.sphere.reg /export/data1/tools/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1231 labels changed using aseg relabeling using gibbs priors... 000: 3221 changed, 138624 examined... 001: 753 changed, 13706 examined... 002: 186 changed, 4149 examined... 003: 68 changed, 1119 examined... 004: 25 changed, 392 examined... 005: 5 changed, 144 examined... 006: 1 changed, 22 examined... 007: 0 changed, 8 examined... 285 labels changed using aseg 000: 130 total segments, 86 labels (351 vertices) changed 001: 46 total segments, 2 labels (2 vertices) changed 002: 44 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 65 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1688 vertices marked for relabeling... 1688 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 46 seconds. #----------------------------------------- #@# Parcellation Stats lh Wed Aug 17 23:30:16 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 NF108_11 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white... reading input pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial... reading input white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 1685 1169 3299 2.699 0.569 0.116 0.031 15 2.2 bankssts 1164 765 2146 2.544 0.834 0.145 0.041 23 1.8 caudalanteriorcingulate 3265 2226 7067 2.748 0.760 0.146 0.064 56 8.1 caudalmiddlefrontal 2036 1474 4582 2.758 0.723 0.194 0.104 61 9.1 cuneus 841 592 2638 2.960 0.989 0.195 0.182 30 3.9 entorhinal 6368 4359 15453 2.984 0.717 0.155 0.074 218 17.6 fusiform 8126 5563 23988 3.365 0.956 0.169 0.116 413 35.2 inferiorparietal 6713 4523 16716 2.939 0.845 0.164 0.159 353 27.9 inferiortemporal 1465 949 3240 2.964 0.884 0.162 0.075 36 4.6 isthmuscingulate 8058 5470 17076 2.642 0.758 0.174 0.099 313 29.6 lateraloccipital 3639 2463 8772 2.740 0.878 0.171 0.109 189 15.8 lateralorbitofrontal 4398 2945 8591 2.614 0.742 0.181 0.146 142 20.2 lingual 2856 1853 6676 3.063 1.081 0.165 0.214 150 30.1 medialorbitofrontal 5037 3430 13441 2.959 0.852 0.158 0.140 195 36.3 middletemporal 1314 853 3228 3.162 0.732 0.117 0.038 12 1.9 parahippocampal 2090 1471 4761 2.711 0.758 0.156 0.062 36 5.0 paracentral 2724 1835 6305 2.683 0.734 0.150 0.065 58 6.7 parsopercularis 976 655 3156 3.273 0.885 0.187 0.103 29 3.9 parsorbitalis 1749 1209 3961 2.508 0.982 0.143 0.066 31 4.5 parstriangularis 1757 1200 3008 2.405 0.867 0.169 0.095 49 5.9 pericalcarine 6655 4468 13338 2.526 0.868 0.167 0.122 212 23.9 postcentral 1832 1219 3849 2.789 0.802 0.156 0.062 38 4.6 posteriorcingulate 6700 4432 14566 2.826 0.683 0.140 0.060 118 14.6 precentral 5395 3773 13724 3.000 0.864 0.150 0.073 103 15.7 precuneus 1268 831 3146 3.196 0.939 0.164 0.093 33 4.8 rostralanteriorcingulate 8238 5526 19791 2.701 0.894 0.172 0.275 413 31.3 rostralmiddlefrontal 9756 6679 25383 3.110 0.898 0.147 0.069 213 23.9 superiorfrontal 8134 5541 18941 2.809 0.814 0.155 0.085 222 25.1 superiorparietal 5347 3680 13575 3.016 0.706 0.153 0.084 174 15.0 superiortemporal 6600 4511 16840 2.942 0.882 0.165 0.094 364 24.0 supramarginal 419 307 1155 2.588 0.976 0.221 0.125 14 2.3 frontalpole 751 569 2655 3.089 1.026 0.176 0.112 18 2.8 temporalpole 739 452 1423 3.024 0.500 0.137 0.049 11 1.6 transversetemporal 3293 2144 8424 3.498 1.031 0.119 0.068 64 9.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Wed Aug 17 23:30:31 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 lh ../surf/lh.sphere.reg /export/data1/tools/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 9 labels changed using aseg relabeling using gibbs priors... 000: 9239 changed, 138624 examined... 001: 2249 changed, 35595 examined... 002: 714 changed, 11580 examined... 003: 284 changed, 4022 examined... 004: 144 changed, 1659 examined... 005: 83 changed, 845 examined... 006: 51 changed, 461 examined... 007: 23 changed, 271 examined... 008: 11 changed, 141 examined... 009: 3 changed, 64 examined... 010: 1 changed, 16 examined... 011: 0 changed, 6 examined... 8 labels changed using aseg 000: 332 total segments, 251 labels (2851 vertices) changed 001: 100 total segments, 20 labels (41 vertices) changed 002: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 141 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 983 vertices marked for relabeling... 983 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 53 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Wed Aug 17 23:31:24 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 NF108_11 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white... reading input pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial... reading input white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 890 606 2063 2.526 0.898 0.189 0.101 22 3.6 G_and_S_frontomargin 1837 1286 4250 2.636 0.831 0.195 0.128 170 8.1 G_and_S_occipital_inf 1319 881 3258 2.817 0.724 0.168 0.085 28 4.4 G_and_S_paracentral 1700 1141 4591 3.096 0.756 0.173 0.101 65 5.0 G_and_S_subcentral 839 594 2887 3.472 1.020 0.179 0.093 23 3.3 G_and_S_transv_frontopol 2371 1603 5270 2.869 0.896 0.149 0.092 63 7.8 G_and_S_cingul-Ant 1667 1138 3264 2.562 0.708 0.136 0.041 26 2.9 G_and_S_cingul-Mid-Ant 1678 1130 3388 2.778 0.773 0.137 0.051 24 3.4 G_and_S_cingul-Mid-Post 454 309 1538 3.403 0.818 0.198 0.086 14 1.6 G_cingul-Post-dorsal 263 173 704 3.134 0.744 0.175 0.086 6 0.7 G_cingul-Post-ventral 1745 1266 4532 2.931 0.841 0.217 0.141 78 9.5 G_cuneus 1621 1101 4533 2.963 0.705 0.163 0.069 39 4.3 G_front_inf-Opercular 388 239 1324 3.539 0.670 0.205 0.142 16 2.3 G_front_inf-Orbital 971 662 3388 3.234 0.896 0.194 0.117 35 4.4 G_front_inf-Triangul 4491 2989 12963 3.020 0.812 0.193 0.129 164 22.2 G_front_middle 6493 4431 19796 3.427 0.776 0.169 0.094 187 20.3 G_front_sup 447 273 1513 4.244 0.755 0.121 0.085 9 1.5 G_Ins_lg_and_S_cent_ins 674 418 2776 4.421 0.563 0.137 0.095 17 2.9 G_insular_short 2545 1763 8439 3.354 0.945 0.201 0.118 85 12.1 G_occipital_middle 1791 1198 4130 2.818 0.737 0.186 0.122 55 8.6 G_occipital_sup 2671 1771 7566 3.192 0.601 0.167 0.078 70 7.8 G_oc-temp_lat-fusifor 3066 2032 6507 2.579 0.796 0.203 0.189 127 17.2 G_oc-temp_med-Lingual 1979 1327 6317 3.426 0.925 0.168 0.093 61 7.5 G_oc-temp_med-Parahip 2625 1718 8128 3.098 0.875 0.203 0.702 377 15.6 G_orbital 3222 2185 12087 3.744 0.859 0.178 0.108 88 14.3 G_pariet_inf-Angular 3797 2604 11188 3.123 0.914 0.184 0.123 327 17.9 G_pariet_inf-Supramar 3547 2442 9857 2.924 0.853 0.167 0.109 147 12.4 G_parietal_sup 2561 1681 5549 2.600 0.875 0.200 0.213 141 14.5 G_postcentral 2519 1614 6900 3.074 0.592 0.157 0.079 54 7.5 G_precentral 2632 1888 9197 3.533 0.774 0.193 0.108 80 12.0 G_precuneus 931 625 2510 2.829 0.913 0.182 0.094 37 4.0 G_rectus 472 281 1016 3.373 0.950 0.156 0.259 50 3.9 G_subcallosal 584 362 1372 3.046 0.453 0.148 0.053 11 1.3 G_temp_sup-G_T_transv 2106 1471 7170 3.199 0.745 0.201 0.162 141 10.1 G_temp_sup-Lateral 538 350 1496 3.705 0.888 0.114 0.047 6 1.0 G_temp_sup-Plan_polar 892 629 2224 2.773 0.685 0.137 0.042 11 1.5 G_temp_sup-Plan_tempo 4306 2866 11755 2.995 0.916 0.183 0.221 324 23.7 G_temporal_inf 3279 2250 10051 3.075 0.863 0.173 0.212 177 33.7 G_temporal_middle 269 180 335 1.876 0.519 0.102 0.021 1 0.3 Lat_Fis-ant-Horizont 284 197 614 2.600 0.668 0.126 0.034 3 0.4 Lat_Fis-ant-Vertical 1221 815 1863 2.540 0.587 0.127 0.042 12 2.1 Lat_Fis-post 2467 1634 4665 2.442 0.640 0.166 0.101 63 8.2 Pole_occipital 2252 1601 6964 2.852 1.005 0.188 0.147 75 9.5 Pole_temporal 2369 1585 3815 2.490 0.721 0.160 0.077 45 7.7 S_calcarine 3010 2038 4189 2.222 0.524 0.130 0.050 30 5.5 S_central 1066 780 2172 2.527 0.764 0.131 0.040 12 1.5 S_cingul-Marginalis 567 387 1058 2.709 0.661 0.101 0.025 3 0.6 S_circular_insula_ant 1484 1013 3015 3.307 0.733 0.099 0.034 21 2.5 S_circular_insula_inf 2016 1385 3487 2.625 0.768 0.109 0.033 16 2.9 S_circular_insula_sup 1293 903 2536 3.085 0.523 0.111 0.031 9 1.7 S_collat_transv_ant 405 283 598 2.089 0.418 0.129 0.050 4 0.9 S_collat_transv_post 3302 2262 5450 2.230 0.747 0.134 0.050 53 6.5 S_front_inf 849 609 1914 2.876 0.835 0.160 0.093 14 2.2 S_front_middle 2491 1731 4038 2.276 0.647 0.109 0.029 16 3.0 S_front_sup 452 293 776 2.593 0.962 0.153 0.062 7 1.3 S_interm_prim-Jensen 2415 1626 4329 2.856 0.705 0.129 0.047 27 4.5 S_intrapariet_and_P_trans 736 495 1534 2.855 0.849 0.149 0.060 10 1.7 S_oc_middle_and_Lunatus 1286 856 2081 2.694 0.706 0.140 0.059 22 3.3 S_oc_sup_and_transversal 1080 754 1700 2.483 0.528 0.136 0.049 13 2.0 S_occipital_ant 1037 735 1856 2.749 0.594 0.126 0.038 10 1.5 S_oc-temp_lat 2326 1588 3959 2.762 0.544 0.126 0.054 109 5.0 S_oc-temp_med_and_Lingual 377 259 805 2.732 0.943 0.136 0.049 4 0.8 S_orbital_lateral 717 494 1478 2.869 1.292 0.135 0.347 21 17.8 S_orbital_med-olfact 1175 807 2144 2.386 0.806 0.153 0.067 20 3.1 S_orbital-H_Shaped 2154 1478 3791 2.627 0.641 0.119 0.037 20 3.4 S_parieto_occipital 1375 832 1829 2.563 0.891 0.143 0.055 34 3.1 S_pericallosal 3015 2080 4572 2.223 0.703 0.123 0.039 28 4.7 S_postcentral 1532 1023 2383 2.539 0.574 0.119 0.033 14 2.2 S_precentral-inf-part 814 563 1259 2.603 0.654 0.116 0.032 6 1.1 S_precentral-sup-part 559 378 1221 2.912 1.027 0.148 0.065 10 1.3 S_suborbital 1030 695 1787 2.499 0.662 0.123 0.045 12 1.8 S_subparietal 1711 1166 2668 2.568 0.587 0.124 0.040 13 2.8 S_temporal_inf 5889 4022 11731 2.882 0.750 0.138 0.075 292 17.4 S_temporal_sup 452 293 802 2.679 0.648 0.094 0.023 3 0.4 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Wed Aug 17 23:31:41 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 modified | TOTAL: 6 pass 1 (xz-): 2 found - 2 modified | TOTAL: 8 pass 2 (xz-): 0 found - 2 modified | TOTAL: 8 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 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 (--): 1 found - 1 modified | TOTAL: 4 pass 2 (--): 0 found - 1 modified | TOTAL: 4 pass 1 (-+): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 Iteration Number : 3 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 : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 16 (out of 241839: 0.006616) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ slice 30: 167 vertices, 202 faces slice 40: 4193 vertices, 4457 faces slice 50: 12487 vertices, 12857 faces slice 60: 22949 vertices, 23363 faces slice 70: 34564 vertices, 35051 faces slice 80: 46355 vertices, 46810 faces slice 90: 58266 vertices, 58771 faces slice 100: 70488 vertices, 71007 faces slice 110: 81827 vertices, 82341 faces slice 120: 92753 vertices, 93275 faces slice 130: 103603 vertices, 104125 faces slice 140: 113761 vertices, 114208 faces slice 150: 122034 vertices, 122466 faces slice 160: 129257 vertices, 129651 faces slice 170: 135549 vertices, 135915 faces slice 180: 140224 vertices, 140546 faces slice 190: 143526 vertices, 143801 faces slice 200: 144400 vertices, 144572 faces slice 210: 144400 vertices, 144572 faces slice 220: 144400 vertices, 144572 faces slice 230: 144400 vertices, 144572 faces slice 240: 144400 vertices, 144572 faces slice 250: 144400 vertices, 144572 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... 144400 voxel in cpt #1: X=-172 [v=144400,e=433716,f=289144] located at (24.241829, -24.853012, 29.193491) For the whole surface: X=-172 [v=144400,e=433716,f=289144] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed Aug 17 23:31:50 EDT 2011 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 Wed Aug 17 23:31:55 EDT 2011 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts avg radius = 47.4 mm, total surface area = 75098 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.070 (target=0.015) step 015: RMS=0.062 (target=0.015) step 020: RMS=0.056 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.048 (target=0.015) step 035: RMS=0.044 (target=0.015) step 040: RMS=0.043 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.041 (target=0.015) step 055: RMS=0.040 (target=0.015) step 060: RMS=0.040 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Aug 17 23:32:53 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.60 (0.00-->5.92) (max @ vno 103282 --> 104420) face area 0.02 +- 0.03 (-0.07-->0.57) scaling brain by 0.300... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.996, avgs=0 005/300: dt: 0.9000, rms radial error=176.741, avgs=0 010/300: dt: 0.9000, rms radial error=176.193, avgs=0 015/300: dt: 0.9000, rms radial error=175.471, avgs=0 020/300: dt: 0.9000, rms radial error=174.640, avgs=0 025/300: dt: 0.9000, rms radial error=173.752, avgs=0 030/300: dt: 0.9000, rms radial error=172.832, avgs=0 035/300: dt: 0.9000, rms radial error=171.896, avgs=0 040/300: dt: 0.9000, rms radial error=170.951, avgs=0 045/300: dt: 0.9000, rms radial error=170.004, avgs=0 050/300: dt: 0.9000, rms radial error=169.058, avgs=0 055/300: dt: 0.9000, rms radial error=168.114, avgs=0 060/300: dt: 0.9000, rms radial error=167.174, avgs=0 065/300: dt: 0.9000, rms radial error=166.238, avgs=0 070/300: dt: 0.9000, rms radial error=165.307, avgs=0 075/300: dt: 0.9000, rms radial error=164.381, avgs=0 080/300: dt: 0.9000, rms radial error=163.459, avgs=0 085/300: dt: 0.9000, rms radial error=162.542, avgs=0 090/300: dt: 0.9000, rms radial error=161.631, avgs=0 095/300: dt: 0.9000, rms radial error=160.724, avgs=0 100/300: dt: 0.9000, rms radial error=159.822, avgs=0 105/300: dt: 0.9000, rms radial error=158.924, avgs=0 110/300: dt: 0.9000, rms radial error=158.031, avgs=0 115/300: dt: 0.9000, rms radial error=157.143, avgs=0 120/300: dt: 0.9000, rms radial error=156.259, avgs=0 125/300: dt: 0.9000, rms radial error=155.380, avgs=0 130/300: dt: 0.9000, rms radial error=154.506, avgs=0 135/300: dt: 0.9000, rms radial error=153.637, avgs=0 140/300: dt: 0.9000, rms radial error=152.772, avgs=0 145/300: dt: 0.9000, rms radial error=151.911, avgs=0 150/300: dt: 0.9000, rms radial error=151.055, avgs=0 155/300: dt: 0.9000, rms radial error=150.204, avgs=0 160/300: dt: 0.9000, rms radial error=149.358, avgs=0 165/300: dt: 0.9000, rms radial error=148.516, avgs=0 170/300: dt: 0.9000, rms radial error=147.679, avgs=0 175/300: dt: 0.9000, rms radial error=146.846, avgs=0 180/300: dt: 0.9000, rms radial error=146.018, avgs=0 185/300: dt: 0.9000, rms radial error=145.194, avgs=0 190/300: dt: 0.9000, rms radial error=144.376, avgs=0 195/300: dt: 0.9000, rms radial error=143.561, avgs=0 200/300: dt: 0.9000, rms radial error=142.752, avgs=0 205/300: dt: 0.9000, rms radial error=141.946, avgs=0 210/300: dt: 0.9000, rms radial error=141.146, avgs=0 215/300: dt: 0.9000, rms radial error=140.349, avgs=0 220/300: dt: 0.9000, rms radial error=139.557, avgs=0 225/300: dt: 0.9000, rms radial error=138.769, avgs=0 230/300: dt: 0.9000, rms radial error=137.986, avgs=0 235/300: dt: 0.9000, rms radial error=137.207, avgs=0 240/300: dt: 0.9000, rms radial error=136.432, avgs=0 245/300: dt: 0.9000, rms radial error=135.662, avgs=0 250/300: dt: 0.9000, rms radial error=134.895, avgs=0 255/300: dt: 0.9000, rms radial error=134.134, avgs=0 260/300: dt: 0.9000, rms radial error=133.376, avgs=0 265/300: dt: 0.9000, rms radial error=132.622, avgs=0 270/300: dt: 0.9000, rms radial error=131.873, avgs=0 275/300: dt: 0.9000, rms radial error=131.128, avgs=0 280/300: dt: 0.9000, rms radial error=130.387, avgs=0 285/300: dt: 0.9000, rms radial error=129.650, avgs=0 290/300: dt: 0.9000, rms radial error=128.917, avgs=0 295/300: dt: 0.9000, rms radial error=128.188, avgs=0 300/300: dt: 0.9000, rms radial error=127.464, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 7505.24 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 2 (K=80.0), pass 1, starting sse = 1077.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00027 epoch 3 (K=320.0), pass 1, starting sse = 107.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/10 = 0.00591 epoch 4 (K=1280.0), pass 1, starting sse = 12.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/13 = 0.00566 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed Aug 17 23:38:42 EDT 2011 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 NF108_11 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 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-172 (nv=144400, nf=289144, ne=433716, g=87) 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 11 iterations marking ambiguous vertices... 11203 ambiguous faces found in tessellation segmenting defects... 86 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 3 -merging segment 4 into 3 -merging segment 18 into 15 -merging segment 32 into 30 -merging segment 42 into 40 -merging segment 44 into 40 -merging segment 65 into 61 79 defects to be corrected 0 vertices coincident reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5294 (-4.7647) -vertex loglikelihood: -6.4095 (-3.2048) -normal dot loglikelihood: -3.6048 (-3.6048) -quad curv loglikelihood: -6.0340 (-3.0170) Total Loglikelihood : -25.5777 CORRECTING DEFECT 0 (vertices=38, convex hull=60) After retessellation of defect 0, euler #=-80 (137560,409716,272076) : difference with theory (-76) = 4 CORRECTING DEFECT 1 (vertices=53, convex hull=83) After retessellation of defect 1, euler #=-79 (137573,409787,272135) : difference with theory (-75) = 4 CORRECTING DEFECT 2 (vertices=29, convex hull=40) After retessellation of defect 2, euler #=-78 (137583,409832,272171) : difference with theory (-74) = 4 CORRECTING DEFECT 3 (vertices=495, convex hull=318) After retessellation of defect 3, euler #=-75 (137688,410314,272551) : difference with theory (-73) = 2 CORRECTING DEFECT 4 (vertices=279, convex hull=202) After retessellation of defect 4, euler #=-75 (137735,410557,272747) : difference with theory (-72) = 3 CORRECTING DEFECT 5 (vertices=7, convex hull=29) After retessellation of defect 5, euler #=-74 (137736,410569,272759) : difference with theory (-71) = 3 CORRECTING DEFECT 6 (vertices=158, convex hull=143) After retessellation of defect 6, euler #=-73 (137799,410831,272959) : difference with theory (-70) = 3 CORRECTING DEFECT 7 (vertices=16, convex hull=33) After retessellation of defect 7, euler #=-72 (137800,410846,272974) : difference with theory (-69) = 3 CORRECTING DEFECT 8 (vertices=25, convex hull=63) After retessellation of defect 8, euler #=-71 (137813,410913,273029) : difference with theory (-68) = 3 CORRECTING DEFECT 9 (vertices=203, convex hull=165) After retessellation of defect 9, euler #=-70 (137867,411151,273214) : difference with theory (-67) = 3 CORRECTING DEFECT 10 (vertices=103, convex hull=101) After retessellation of defect 10, euler #=-69 (137897,411291,273325) : difference with theory (-66) = 3 CORRECTING DEFECT 11 (vertices=108, convex hull=159) After retessellation of defect 11, euler #=-68 (137924,411448,273456) : difference with theory (-65) = 3 CORRECTING DEFECT 12 (vertices=170, convex hull=160) After retessellation of defect 12, euler #=-67 (137963,411637,273607) : difference with theory (-64) = 3 CORRECTING DEFECT 13 (vertices=277, convex hull=223) After retessellation of defect 13, euler #=-65 (138053,412020,273902) : difference with theory (-63) = 2 CORRECTING DEFECT 14 (vertices=83, convex hull=90) After retessellation of defect 14, euler #=-64 (138071,412110,273975) : difference with theory (-62) = 2 CORRECTING DEFECT 15 (vertices=69, convex hull=77) After retessellation of defect 15, euler #=-63 (138090,412194,274041) : difference with theory (-61) = 2 CORRECTING DEFECT 16 (vertices=8, convex hull=33) After retessellation of defect 16, euler #=-62 (138090,412206,274054) : difference with theory (-60) = 2 CORRECTING DEFECT 17 (vertices=76, convex hull=98) After retessellation of defect 17, euler #=-61 (138120,412334,274153) : difference with theory (-59) = 2 CORRECTING DEFECT 18 (vertices=30, convex hull=54) After retessellation of defect 18, euler #=-60 (138129,412378,274189) : difference with theory (-58) = 2 CORRECTING DEFECT 19 (vertices=13, convex hull=29) After retessellation of defect 19, euler #=-59 (138131,412395,274205) : difference with theory (-57) = 2 CORRECTING DEFECT 20 (vertices=77, convex hull=106) After retessellation of defect 20, euler #=-58 (138155,412516,274303) : difference with theory (-56) = 2 CORRECTING DEFECT 21 (vertices=8, convex hull=25) After retessellation of defect 21, euler #=-57 (138155,412523,274311) : difference with theory (-55) = 2 CORRECTING DEFECT 22 (vertices=47, convex hull=86) After retessellation of defect 22, euler #=-56 (138164,412586,274366) : difference with theory (-54) = 2 CORRECTING DEFECT 23 (vertices=205, convex hull=96) After retessellation of defect 23, euler #=-55 (138200,412738,274483) : difference with theory (-53) = 2 CORRECTING DEFECT 24 (vertices=81, convex hull=99) After retessellation of defect 24, euler #=-54 (138233,412885,274598) : difference with theory (-52) = 2 CORRECTING DEFECT 25 (vertices=28, convex hull=65) After retessellation of defect 25, euler #=-53 (138242,412937,274642) : difference with theory (-51) = 2 CORRECTING DEFECT 26 (vertices=8, convex hull=31) After retessellation of defect 26, euler #=-52 (138243,412947,274652) : difference with theory (-50) = 2 CORRECTING DEFECT 27 (vertices=49, convex hull=64) After retessellation of defect 27, euler #=-50 (138250,412996,274696) : difference with theory (-49) = 1 CORRECTING DEFECT 28 (vertices=37, convex hull=76) After retessellation of defect 28, euler #=-49 (138272,413096,274775) : difference with theory (-48) = 1 CORRECTING DEFECT 29 (vertices=184, convex hull=106) After retessellation of defect 29, euler #=-48 (138296,413222,274878) : difference with theory (-47) = 1 CORRECTING DEFECT 30 (vertices=56, convex hull=94) After retessellation of defect 30, euler #=-47 (138328,413367,274992) : difference with theory (-46) = 1 CORRECTING DEFECT 31 (vertices=66, convex hull=114) After retessellation of defect 31, euler #=-46 (138354,413499,275099) : difference with theory (-45) = 1 CORRECTING DEFECT 32 (vertices=57, convex hull=93) After retessellation of defect 32, euler #=-45 (138368,413582,275169) : difference with theory (-44) = 1 CORRECTING DEFECT 33 (vertices=43, convex hull=29) After retessellation of defect 33, euler #=-44 (138371,413599,275184) : difference with theory (-43) = 1 CORRECTING DEFECT 34 (vertices=37, convex hull=77) After retessellation of defect 34, euler #=-43 (138395,413702,275264) : difference with theory (-42) = 1 CORRECTING DEFECT 35 (vertices=18, convex hull=32) After retessellation of defect 35, euler #=-42 (138398,413722,275282) : difference with theory (-41) = 1 CORRECTING DEFECT 36 (vertices=127, convex hull=192) After retessellation of defect 36, euler #=-39 (138464,414018,275515) : difference with theory (-40) = -1 CORRECTING DEFECT 37 (vertices=47, convex hull=102) After retessellation of defect 37, euler #=-38 (138497,414165,275630) : difference with theory (-39) = -1 CORRECTING DEFECT 38 (vertices=166, convex hull=172) After retessellation of defect 38, euler #=-37 (138575,414474,275862) : difference with theory (-38) = -1 CORRECTING DEFECT 39 (vertices=60, convex hull=89) After retessellation of defect 39, euler #=-36 (138593,414566,275937) : difference with theory (-37) = -1 CORRECTING DEFECT 40 (vertices=73, convex hull=120) After retessellation of defect 40, euler #=-35 (138624,414710,276051) : difference with theory (-36) = -1 CORRECTING DEFECT 41 (vertices=16, convex hull=56) After retessellation of defect 41, euler #=-34 (138634,414760,276092) : difference with theory (-35) = -1 CORRECTING DEFECT 42 (vertices=226, convex hull=147) After retessellation of defect 42, euler #=-33 (138651,414880,276196) : difference with theory (-34) = -1 CORRECTING DEFECT 43 (vertices=24, convex hull=26) After retessellation of defect 43, euler #=-32 (138653,414897,276212) : difference with theory (-33) = -1 CORRECTING DEFECT 44 (vertices=95, convex hull=33) After retessellation of defect 44, euler #=-31 (138662,414935,276242) : difference with theory (-32) = -1 CORRECTING DEFECT 45 (vertices=5, convex hull=21) After retessellation of defect 45, euler #=-30 (138662,414941,276249) : difference with theory (-31) = -1 CORRECTING DEFECT 46 (vertices=16, convex hull=44) After retessellation of defect 46, euler #=-29 (138671,414980,276280) : difference with theory (-30) = -1 CORRECTING DEFECT 47 (vertices=21, convex hull=49) After retessellation of defect 47, euler #=-28 (138683,415034,276323) : difference with theory (-29) = -1 CORRECTING DEFECT 48 (vertices=6, convex hull=21) After retessellation of defect 48, euler #=-27 (138683,415040,276330) : difference with theory (-28) = -1 CORRECTING DEFECT 49 (vertices=58, convex hull=85) After retessellation of defect 49, euler #=-26 (138697,415116,276393) : difference with theory (-27) = -1 CORRECTING DEFECT 50 (vertices=18, convex hull=15) After retessellation of defect 50, euler #=-25 (138699,415125,276401) : difference with theory (-26) = -1 CORRECTING DEFECT 51 (vertices=109, convex hull=52) After retessellation of defect 51, euler #=-24 (138719,415209,276466) : difference with theory (-25) = -1 CORRECTING DEFECT 52 (vertices=148, convex hull=70) After retessellation of defect 52, euler #=-23 (138746,415318,276549) : difference with theory (-24) = -1 CORRECTING DEFECT 53 (vertices=25, convex hull=55) After retessellation of defect 53, euler #=-22 (138755,415365,276588) : difference with theory (-23) = -1 CORRECTING DEFECT 54 (vertices=8, convex hull=20) After retessellation of defect 54, euler #=-21 (138756,415374,276597) : difference with theory (-22) = -1 CORRECTING DEFECT 55 (vertices=149, convex hull=205) After retessellation of defect 55, euler #=-20 (138851,415757,276886) : difference with theory (-21) = -1 CORRECTING DEFECT 56 (vertices=53, convex hull=51) After retessellation of defect 56, euler #=-19 (138871,415839,276949) : difference with theory (-20) = -1 CORRECTING DEFECT 57 (vertices=10, convex hull=34) After retessellation of defect 57, euler #=-18 (138874,415858,276966) : difference with theory (-19) = -1 CORRECTING DEFECT 58 (vertices=985, convex hull=390) After retessellation of defect 58, euler #=-18 (139019,416499,277462) : difference with theory (-18) = 0 CORRECTING DEFECT 59 (vertices=37, convex hull=44) After retessellation of defect 59, euler #=-17 (139029,416548,277502) : difference with theory (-17) = 0 CORRECTING DEFECT 60 (vertices=52, convex hull=97) After retessellation of defect 60, euler #=-16 (139049,416649,277584) : difference with theory (-16) = 0 CORRECTING DEFECT 61 (vertices=49, convex hull=42) After retessellation of defect 61, euler #=-15 (139063,416704,277626) : difference with theory (-15) = 0 CORRECTING DEFECT 62 (vertices=37, convex hull=42) After retessellation of defect 62, euler #=-14 (139070,416744,277660) : difference with theory (-14) = 0 CORRECTING DEFECT 63 (vertices=63, convex hull=42) After retessellation of defect 63, euler #=-13 (139081,416793,277699) : difference with theory (-13) = 0 CORRECTING DEFECT 64 (vertices=48, convex hull=74) After retessellation of defect 64, euler #=-12 (139095,416868,277761) : difference with theory (-12) = 0 CORRECTING DEFECT 65 (vertices=5, convex hull=20) After retessellation of defect 65, euler #=-11 (139095,416873,277767) : difference with theory (-11) = 0 CORRECTING DEFECT 66 (vertices=22, convex hull=61) After retessellation of defect 66, euler #=-10 (139110,416942,277822) : difference with theory (-10) = 0 CORRECTING DEFECT 67 (vertices=68, convex hull=74) After retessellation of defect 67, euler #=-9 (139128,417023,277886) : difference with theory (-9) = 0 CORRECTING DEFECT 68 (vertices=27, convex hull=49) After retessellation of defect 68, euler #=-8 (139138,417069,277923) : difference with theory (-8) = 0 CORRECTING DEFECT 69 (vertices=112, convex hull=102) After retessellation of defect 69, euler #=-7 (139153,417156,277996) : difference with theory (-7) = 0 CORRECTING DEFECT 70 (vertices=94, convex hull=85) After retessellation of defect 70, euler #=-6 (139167,417236,278063) : difference with theory (-6) = 0 CORRECTING DEFECT 71 (vertices=234, convex hull=156) After retessellation of defect 71, euler #=-5 (139191,417388,278192) : difference with theory (-5) = 0 CORRECTING DEFECT 72 (vertices=30, convex hull=61) After retessellation of defect 72, euler #=-4 (139203,417448,278241) : difference with theory (-4) = 0 CORRECTING DEFECT 73 (vertices=113, convex hull=94) After retessellation of defect 73, euler #=-3 (139221,417543,278319) : difference with theory (-3) = 0 CORRECTING DEFECT 74 (vertices=31, convex hull=67) After retessellation of defect 74, euler #=-2 (139236,417614,278376) : difference with theory (-2) = 0 CORRECTING DEFECT 75 (vertices=35, convex hull=87) After retessellation of defect 75, euler #=-1 (139251,417694,278442) : difference with theory (-1) = 0 CORRECTING DEFECT 76 (vertices=25, convex hull=34) After retessellation of defect 76, euler #=0 (139253,417709,278456) : difference with theory (0) = 0 CORRECTING DEFECT 77 (vertices=50, convex hull=85) After retessellation of defect 77, euler #=1 (139278,417820,278543) : difference with theory (1) = 0 CORRECTING DEFECT 78 (vertices=24, convex hull=26) After retessellation of defect 78, euler #=2 (139279,417831,278554) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.04-->14.22) (max @ vno 125712 --> 132153) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.04-->14.22) (max @ vno 125712 --> 132153) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 281 mutations (35.5%), 510 crossovers (64.5%), 434 vertices were eliminated building final representation... 5121 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=139279, nf=278554, ne=417831, g=0) writing corrected surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 61.2 minutes 0 defective edges removing intersecting faces 000: 743 intersecting 001: 34 intersecting 002: 4 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 139279 - 417831 + 278554 = 2 --> 0 holes F =2V-4: 278554 = 278558-4 (0) 2E=3F: 835662 = 835662 (0) total defect index = 0 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 91 intersecting 001: 14 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make Final Surf rh Thu Aug 18 00:40:00 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs NF108_11 rh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/filled.mgz... reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/brain.finalsurfs.mgz... reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... 24438 bright wm thresholded. 10 bright non-wm voxels segmented. reading original surface position from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.orig... computing class statistics... border white: 252840 voxels (1.51%) border gray 310905 voxels (1.85%) WM (96.0): 96.8 +- 8.8 [70.0 --> 110.0] GM (71.0) : 70.4 +- 9.8 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.2 (was 70) setting MAX_BORDER_WHITE to 111.8 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 49.4 (was 40) setting MAX_GRAY to 94.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.7 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.24 (0.02-->6.65) (max @ vno 126275 --> 132649) face area 0.28 +- 0.13 (0.00-->3.48) mean absolute distance = 0.61 +- 0.76 3214 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=69 using class modes intead of means.... mean inside = 92.4, mean outside = 74.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=80.2, 168 (168) missing vertices, mean dist 0.2 [0.5 (%39.5)->0.7 (%60.5))] %73 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.09-->6.27) (max @ vno 132153 --> 132648) face area 0.28 +- 0.14 (0.00-->3.30) mean absolute distance = 0.31 +- 0.52 2885 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5150054.0, rms=9.35 001: dt: 0.5000, sse=6316536.5, rms=6.46 002: dt: 0.5000, sse=7020948.5, rms=5.13 003: dt: 0.5000, sse=7475928.0, rms=4.53 004: dt: 0.5000, sse=7759807.5, rms=4.19 005: dt: 0.5000, sse=7912889.5, rms=4.03 006: dt: 0.5000, sse=7962038.0, rms=3.89 007: dt: 0.5000, sse=7979900.5, rms=3.83 008: dt: 0.5000, sse=8008245.0, rms=3.74 rms = 3.72, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7993266.5, rms=3.72 010: dt: 0.2500, sse=5245946.5, rms=2.66 011: dt: 0.2500, sse=4859529.5, rms=2.38 012: dt: 0.2500, sse=4648952.5, rms=2.31 013: dt: 0.2500, sse=4593024.5, rms=2.26 rms = 2.22, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4538798.0, rms=2.22 015: dt: 0.1250, sse=4454759.5, rms=2.16 rms = 2.15, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4416077.5, rms=2.15 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... mean border=82.9, 178 (32) missing vertices, mean dist -0.1 [0.3 (%70.3)->0.3 (%29.7))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.27 (0.09-->6.25) (max @ vno 132153 --> 132648) face area 0.34 +- 0.17 (0.00-->4.07) mean absolute distance = 0.25 +- 0.42 3303 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4825753.0, rms=4.01 017: dt: 0.5000, sse=5471911.0, rms=2.82 rms = 3.23, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5078565.5, rms=2.13 019: dt: 0.2500, sse=4942303.5, rms=1.84 020: dt: 0.2500, sse=4884254.5, rms=1.75 rms = 1.75, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4838162.5, rms=1.75 rms = 1.70, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4771741.0, rms=1.70 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.4, 173 (18) missing vertices, mean dist -0.1 [0.3 (%61.9)->0.2 (%38.1))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.07-->6.43) (max @ vno 132153 --> 132648) face area 0.34 +- 0.17 (0.00-->3.91) mean absolute distance = 0.24 +- 0.38 3576 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4849925.0, rms=2.48 rms = 2.62, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4828419.0, rms=1.88 024: dt: 0.2500, sse=4911199.0, rms=1.59 rms = 1.56, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4961176.5, rms=1.56 rms = 1.52, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4902518.0, rms=1.52 positioning took 0.5 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 removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=85.0, 171 (12) missing vertices, mean dist -0.0 [0.3 (%52.6)->0.2 (%47.4))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4913499.5, rms=1.68 rms = 1.80, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5058073.0, rms=1.33 028: dt: 0.2500, sse=5361753.5, rms=1.17 rms = 1.18, time step reduction 2 of 3 to 0.125... rms = 1.17, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5366844.5, rms=1.17 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... label Right_Hippocampus: removing 7349 voxels in segment 0 label Right_Hippocampus: removing 73 voxels in segment 1 label Right_Hippocampus: removing 1695 voxels in segment 2 label Right_Hippocampus: removing 2 voxels in segment 3 label Right_Hippocampus: removing 8 voxels in segment 4 label Right_Hippocampus: removing 27 voxels in segment 5 label Right_Hippocampus: removing 32 voxels in segment 6 label Right_Hippocampus: removing 1 voxels in segment 7 label Right_Hippocampus: removing 14 voxels in segment 9 label Right_Hippocampus: removing 192 voxels in segment 10 label Right_Hippocampus: removing 23061 voxels in segment 11 label Right_Amygdala: removing 183 voxels in segment 1 label Right_Amygdala: removing 893 voxels in segment 2 generating cortex label... 17 non-cortical segments detected only using segment with 1755 vertices erasing segment 1 (vno[0] = 57953) erasing segment 2 (vno[0] = 72072) erasing segment 3 (vno[0] = 90353) erasing segment 4 (vno[0] = 91567) erasing segment 5 (vno[0] = 97778) erasing segment 6 (vno[0] = 99709) erasing segment 7 (vno[0] = 101046) erasing segment 8 (vno[0] = 101797) erasing segment 9 (vno[0] = 102777) erasing segment 10 (vno[0] = 102923) erasing segment 11 (vno[0] = 103791) erasing segment 12 (vno[0] = 107647) erasing segment 13 (vno[0] = 110168) erasing segment 14 (vno[0] = 111025) erasing segment 15 (vno[0] = 111897) erasing segment 16 (vno[0] = 112688) writing cortex label to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/label/rh.cortex.label... LabelWrite: saving to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/label/rh.cortex.label writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.curv writing smoothed area to rh.area writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.area vertex spacing 0.90 +- 0.27 (0.08-->6.34) (max @ vno 132153 --> 132648) face area 0.34 +- 0.17 (0.00-->3.76) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.4, 180 (180) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.8 (%100.0))] %17 local maxima, %45 large gradients and %34 min vals, 3382 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=19171168.0, rms=24.54 001: dt: 0.5000, sse=14276507.0, rms=20.42 002: dt: 0.5000, sse=10976413.0, rms=17.10 003: dt: 0.5000, sse=9010825.0, rms=14.52 004: dt: 0.5000, sse=7975900.0, rms=12.53 005: dt: 0.5000, sse=7355389.0, rms=10.99 006: dt: 0.5000, sse=6982708.0, rms=9.84 007: dt: 0.5000, sse=6795445.5, rms=8.97 008: dt: 0.5000, sse=6737190.5, rms=8.26 009: dt: 0.5000, sse=6722769.0, rms=7.67 010: dt: 0.5000, sse=6751047.0, rms=7.18 011: dt: 0.5000, sse=6863206.5, rms=6.77 012: dt: 0.5000, sse=6939365.5, rms=6.41 013: dt: 0.5000, sse=7056037.0, rms=6.09 014: dt: 0.5000, sse=7194976.0, rms=5.79 015: dt: 0.5000, sse=7253330.0, rms=5.51 016: dt: 0.5000, sse=7393221.5, rms=5.25 017: dt: 0.5000, sse=7505870.0, rms=5.02 018: dt: 0.5000, sse=7599009.5, rms=4.83 019: dt: 0.5000, sse=7665201.0, rms=4.68 020: dt: 0.5000, sse=7741048.0, rms=4.57 021: dt: 0.5000, sse=7778185.0, rms=4.49 022: dt: 0.5000, sse=7850986.5, rms=4.41 023: dt: 0.5000, sse=7868111.0, rms=4.36 rms = 4.32, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=7874402.0, rms=4.32 025: dt: 0.2500, sse=6657886.0, rms=4.12 026: dt: 0.2500, sse=6547904.0, rms=4.06 rms = 4.05, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=6513131.5, rms=4.05 rms = 4.01, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=6333272.0, rms=4.01 positioning took 3.0 minutes mean border=58.6, 1850 (32) missing vertices, mean dist 0.4 [0.3 (%42.1)->1.2 (%57.9))] %35 local maxima, %30 large gradients and %29 min vals, 1738 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7021882.5, rms=5.44 029: dt: 0.5000, sse=7142550.0, rms=4.96 030: dt: 0.5000, sse=8327263.0, rms=4.70 031: dt: 0.5000, sse=8266998.0, rms=4.58 032: dt: 0.5000, sse=8959358.0, rms=4.44 033: dt: 0.5000, sse=8798353.0, rms=4.35 034: dt: 0.5000, sse=9232103.0, rms=4.26 035: dt: 0.5000, sse=9036502.0, rms=4.21 036: dt: 0.5000, sse=9385153.0, rms=4.15 rms = 4.12, time step reduction 1 of 3 to 0.250... 037: dt: 0.5000, sse=9176419.0, rms=4.12 038: dt: 0.2500, sse=8026226.0, rms=3.85 039: dt: 0.2500, sse=7925850.0, rms=3.76 rms = 3.77, time step reduction 2 of 3 to 0.125... rms = 3.74, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=7856429.5, rms=3.74 positioning took 1.4 minutes mean border=57.6, 2459 (22) missing vertices, mean dist 0.2 [0.3 (%39.1)->0.7 (%60.9))] %47 local maxima, %18 large gradients and %29 min vals, 1974 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=8002731.5, rms=4.13 rms = 4.10, time step reduction 1 of 3 to 0.250... 041: dt: 0.5000, sse=8355706.0, rms=4.10 042: dt: 0.2500, sse=8002086.5, rms=3.79 043: dt: 0.2500, sse=8060320.0, rms=3.70 rms = 3.68, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=8103464.0, rms=3.68 045: dt: 0.1250, sse=7951599.5, rms=3.60 rms = 3.59, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=7969155.5, rms=3.59 positioning took 0.6 minutes mean border=57.1, 4826 (17) missing vertices, mean dist 0.1 [0.3 (%42.8)->0.5 (%57.2))] %50 local maxima, %14 large gradients and %28 min vals, 1870 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=7983295.0, rms=3.64 rms = 3.70, time step reduction 1 of 3 to 0.250... 047: dt: 0.2500, sse=7935895.5, rms=3.56 048: dt: 0.2500, sse=8187287.0, rms=3.49 rms = 3.46, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=8305067.0, rms=3.46 050: dt: 0.1250, sse=8231142.5, rms=3.39 rms = 3.37, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=8291477.5, rms=3.37 positioning took 0.6 minutes writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.area.pial vertex spacing 1.08 +- 0.50 (0.03-->7.94) (max @ vno 103888 --> 102920) face area 0.46 +- 0.39 (0.00-->7.55) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 139279 vertices processed 25000 of 139279 vertices processed 50000 of 139279 vertices processed 75000 of 139279 vertices processed 100000 of 139279 vertices processed 125000 of 139279 vertices processed 0 of 139279 vertices processed 25000 of 139279 vertices processed 50000 of 139279 vertices processed 75000 of 139279 vertices processed 100000 of 139279 vertices processed 125000 of 139279 vertices processed thickness calculation complete, 4205:5579 truncations. 44401 vertices at 0 distance 61701 vertices at 1 distance 71436 vertices at 2 distance 48571 vertices at 3 distance 23156 vertices at 4 distance 9570 vertices at 5 distance 3899 vertices at 6 distance 1765 vertices at 7 distance 925 vertices at 8 distance 560 vertices at 9 distance 360 vertices at 10 distance 292 vertices at 11 distance 208 vertices at 12 distance 178 vertices at 13 distance 171 vertices at 14 distance 147 vertices at 15 distance 117 vertices at 16 distance 89 vertices at 17 distance 87 vertices at 18 distance 85 vertices at 19 distance 106 vertices at 20 distance writing curvature file /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.thickness positioning took 14.5 minutes #-------------------------------------------- #@# Surf Volume rh Thu Aug 18 00:54:30 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf mris_calc -o rh.area.mid rh.area add rh.area.pial mris_calc -o rh.area.mid rh.area.mid div 2 mris_calc -o rh.volume rh.area.mid mul rh.thickness #-------------------------------------------- #@# Smooth2 rh Thu Aug 18 00:54:31 EDT 2011 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 Thu Aug 18 00:54:35 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.2 mm, total surface area = 85644 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.088 (target=0.015) step 010: RMS=0.068 (target=0.015) step 015: RMS=0.057 (target=0.015) step 020: RMS=0.049 (target=0.015) step 025: RMS=0.042 (target=0.015) step 030: RMS=0.035 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.021 (target=0.015) inflation complete. inflation took 1.0 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 377 vertices thresholded to be in k1 ~ [-0.45 0.29], k2 ~ [-0.13 0.07] total integrated curvature = 0.301*4pi (3.783) --> 1 handles ICI = 1.3, FI = 11.9, variation=189.782 197 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 148 vertices thresholded to be in [-0.19 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Thu Aug 18 00:56:59 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm NF108_11 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 [ NF108_11/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 332 ] WARN: S lookup min: -0.055069 WARN: S explicit min: 0.000000 vertex = 595 #-------------------------------------------- #@# Sphere rh Thu Aug 18 00:57:04 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.69 hours scaling brain by 0.279... pass 1: epoch 1 of 3 starting distance error %20.91 pass 1: epoch 2 of 3 starting distance error %20.85 unfolding complete - removing small folds... starting distance error %20.69 removing remaining folds... final distance error %20.71 480: 0 negative triangles #-------------------------------------------- #@# Surf Reg rh Thu Aug 18 02:38:27 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_register -curv ../surf/rh.sphere /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/rh.sphere.reg... curvature mean = -0.000, std = 0.610 curvature mean = 0.015, std = 0.942 curvature mean = 0.024, std = 0.864 curvature mean = -0.008, std = 0.939 curvature mean = 0.010, std = 0.932 curvature mean = -0.013, std = 0.947 curvature mean = 0.005, std = 0.964 curvature mean = -0.016, std = 0.945 curvature mean = 0.001, std = 0.981 curvature mean = -0.043, std = 0.430 curvature mean = 0.004, std = 0.068 curvature mean = 0.066, std = 0.233 curvature mean = 0.004, std = 0.082 curvature mean = 0.050, std = 0.358 curvature mean = 0.004, std = 0.088 curvature mean = 0.030, std = 0.474 curvature mean = 0.004, std = 0.091 curvature mean = 0.012, std = 0.582 expanding nbhd size to 1 456: 0 negative triangles #-------------------------------------------- #@# Jacobian white rh Thu Aug 18 03:41:22 EDT 2011 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 Thu Aug 18 03:41:24 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mrisp_paint -a 5 /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Thu Aug 18 03:41:26 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 rh ../surf/rh.sphere.reg /export/data1/tools/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1390 labels changed using aseg relabeling using gibbs priors... 000: 3162 changed, 139279 examined... 001: 720 changed, 13343 examined... 002: 167 changed, 4057 examined... 003: 61 changed, 1024 examined... 004: 15 changed, 372 examined... 005: 8 changed, 99 examined... 006: 5 changed, 44 examined... 007: 2 changed, 23 examined... 008: 0 changed, 12 examined... 226 labels changed using aseg 000: 126 total segments, 89 labels (507 vertices) changed 001: 39 total segments, 2 labels (4 vertices) changed 002: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 48 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1741 vertices marked for relabeling... 1741 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats rh Thu Aug 18 03:42:13 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 NF108_11 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white... reading input pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial... reading input white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 1806 1330 4027 2.948 0.560 0.133 0.038 21 2.6 bankssts 1003 711 1796 2.082 0.884 0.148 0.033 16 1.3 caudalanteriorcingulate 3406 2359 7526 2.670 0.798 0.138 0.054 60 7.7 caudalmiddlefrontal 1510 1091 2430 2.116 0.578 0.214 0.197 129 9.4 cuneus 551 370 1653 2.723 1.114 0.189 0.094 14 2.4 entorhinal 4953 3367 11555 2.929 0.687 0.150 0.069 99 13.2 fusiform 10182 7004 28681 3.173 0.876 0.160 0.088 234 33.8 inferiorparietal 5053 3385 12549 3.027 0.885 0.153 0.072 137 14.6 inferiortemporal 1971 1253 4603 3.110 0.949 0.159 0.114 72 8.6 isthmuscingulate 6843 4671 15276 2.736 0.755 0.171 0.095 208 27.4 lateraloccipital 3759 2622 8400 2.759 0.929 0.173 0.112 135 15.6 lateralorbitofrontal 3125 2135 5935 2.529 0.720 0.175 0.096 74 11.4 lingual 2292 1579 5865 3.053 1.113 0.151 0.072 53 6.3 medialorbitofrontal 6355 4215 18801 3.222 0.964 0.151 0.073 148 19.3 middletemporal 1053 687 2421 3.020 0.884 0.125 0.063 16 2.0 parahippocampal 2018 1372 4217 2.597 0.681 0.143 0.101 35 4.8 paracentral 2183 1462 4407 2.408 0.741 0.151 0.065 48 6.0 parsopercularis 1186 768 2926 2.540 0.911 0.184 0.113 42 5.5 parsorbitalis 2515 1722 5944 2.538 1.027 0.156 0.077 63 7.1 parstriangularis 997 727 1330 1.880 0.607 0.175 0.096 20 3.6 pericalcarine 4930 3379 11693 2.735 0.863 0.153 0.072 137 14.3 postcentral 1965 1301 4395 2.800 1.177 0.155 0.067 38 5.0 posteriorcingulate 8649 5751 15987 2.374 0.784 0.142 0.074 219 21.4 precentral 7517 5076 16425 2.852 0.759 0.165 0.137 179 25.4 precuneus 1144 765 2974 3.152 1.062 0.154 0.101 27 4.1 rostralanteriorcingulate 8769 5921 20895 2.591 0.959 0.164 0.110 354 29.1 rostralmiddlefrontal 11354 7824 29363 2.946 0.920 0.146 0.156 756 28.1 superiorfrontal 8317 5596 18636 2.853 0.735 0.171 0.112 194 31.6 superiorparietal 5676 3813 15415 3.237 0.867 0.132 0.051 101 13.1 superiortemporal 5398 3660 13804 3.115 0.867 0.155 0.072 111 14.5 supramarginal 652 427 2316 3.444 0.938 0.195 0.396 31 3.0 frontalpole 566 382 1851 3.115 1.126 0.198 0.144 21 2.8 temporalpole 553 355 1264 3.105 0.472 0.164 0.066 11 1.4 transversetemporal 3443 2287 8845 3.527 0.972 0.144 0.505 176 123.4 insula #----------------------------------------- #@# Cortical Parc 2 rh Thu Aug 18 03:42:31 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 rh ../surf/rh.sphere.reg /export/data1/tools/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 5 labels changed using aseg relabeling using gibbs priors... 000: 10253 changed, 139279 examined... 001: 2549 changed, 39022 examined... 002: 831 changed, 13136 examined... 003: 337 changed, 4506 examined... 004: 173 changed, 1967 examined... 005: 95 changed, 973 examined... 006: 55 changed, 547 examined... 007: 34 changed, 289 examined... 008: 15 changed, 176 examined... 009: 7 changed, 74 examined... 010: 7 changed, 48 examined... 011: 9 changed, 45 examined... 012: 2 changed, 49 examined... 013: 0 changed, 12 examined... 2 labels changed using aseg 000: 346 total segments, 261 labels (2796 vertices) changed 001: 104 total segments, 19 labels (162 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 163 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1075 vertices marked for relabeling... 1075 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 54 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Thu Aug 18 03:43:25 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 NF108_11 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/wm.mgz... reading input surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white... reading input pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial... reading input white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 1244 835 2844 2.455 0.767 0.182 0.140 55 6.2 G_and_S_frontomargin 1145 776 2792 2.873 0.662 0.155 0.092 24 4.1 G_and_S_occipital_inf 1102 762 2808 2.672 0.778 0.185 0.263 104 4.6 G_and_S_paracentral 1632 1119 4700 3.173 0.916 0.165 0.072 36 4.1 G_and_S_subcentral 2010 1341 6581 3.139 0.990 0.187 0.532 374 7.6 G_and_S_transv_frontopol 3040 2071 6667 2.765 0.914 0.144 0.117 302 8.9 G_and_S_cingul-Ant 1564 1090 3230 2.677 0.833 0.133 0.044 23 2.2 G_and_S_cingul-Mid-Ant 1602 1120 4076 2.945 0.918 0.145 0.059 25 3.4 G_and_S_cingul-Mid-Post 713 442 2172 3.504 0.990 0.181 0.120 31 3.0 G_cingul-Post-dorsal 403 249 1037 3.065 0.726 0.187 0.185 31 1.8 G_cingul-Post-ventral 1283 949 2213 2.156 0.556 0.209 0.129 94 7.4 G_cuneus 1344 907 3755 2.866 0.802 0.172 0.081 38 4.4 G_front_inf-Opercular 543 363 1742 3.105 0.988 0.187 0.098 22 2.2 G_front_inf-Orbital 1261 851 3804 2.841 1.045 0.183 0.114 45 4.9 G_front_inf-Triangul 4344 2910 12142 2.887 0.893 0.180 0.147 241 16.9 G_front_middle 6807 4618 20950 3.224 0.899 0.161 0.116 152 21.0 G_front_sup 458 301 1486 4.191 0.843 0.191 3.173 23 112.7 G_Ins_lg_and_S_cent_ins 672 420 2549 3.969 0.758 0.177 0.131 93 4.0 G_insular_short 2160 1443 7328 3.471 0.805 0.186 0.110 59 9.2 G_occipital_middle 2899 1876 5975 2.730 0.627 0.188 0.174 111 16.0 G_occipital_sup 2295 1530 6182 3.144 0.564 0.158 0.075 48 6.2 G_oc-temp_lat-fusifor 2137 1419 4342 2.522 0.782 0.196 0.125 66 9.6 G_oc-temp_med-Lingual 1584 1041 4295 3.172 1.054 0.174 0.121 46 8.1 G_oc-temp_med-Parahip 2697 1801 7502 2.904 0.972 0.212 0.168 165 16.1 G_orbital 4374 3042 16518 3.552 0.876 0.189 0.132 159 19.4 G_pariet_inf-Angular 2798 1891 8502 3.339 0.870 0.172 0.083 71 8.6 G_pariet_inf-Supramar 2349 1582 6259 2.996 0.778 0.163 0.093 50 7.7 G_parietal_sup 1630 1116 4517 2.873 0.782 0.172 0.102 43 7.0 G_postcentral 3369 2184 6071 2.239 0.736 0.151 0.074 69 10.1 G_precentral 4078 2780 10782 3.070 0.802 0.185 0.206 129 18.6 G_precuneus 640 475 2262 3.454 1.022 0.187 0.091 20 2.6 G_rectus 353 240 1141 4.137 0.767 0.139 0.105 17 0.6 G_subcallosal 443 279 1246 3.340 0.597 0.181 0.084 12 1.5 G_temp_sup-G_T_transv 1851 1250 6811 3.534 0.830 0.176 0.088 69 7.6 G_temp_sup-Lateral 771 514 2325 3.694 0.723 0.120 0.058 22 1.4 G_temp_sup-Plan_polar 984 677 2525 3.146 0.594 0.110 0.029 7 1.3 G_temp_sup-Plan_tempo 2374 1569 6975 3.130 0.881 0.181 0.101 100 9.5 G_temporal_inf 4092 2659 14459 3.586 0.854 0.172 0.093 127 16.3 G_temporal_middle 554 365 903 2.217 0.731 0.122 0.040 6 0.9 Lat_Fis-ant-Horizont 172 126 264 2.071 0.470 0.130 0.026 2 0.2 Lat_Fis-ant-Vertical 1702 1153 3012 3.101 0.672 0.128 0.040 17 2.8 Lat_Fis-post 2729 1843 5373 2.458 0.736 0.207 0.159 149 14.5 Pole_occipital 1935 1281 6111 2.944 1.068 0.191 0.124 71 9.4 Pole_temporal 1358 966 2025 2.313 0.726 0.149 0.078 24 3.7 S_calcarine 2180 1485 2965 2.135 0.640 0.129 0.040 24 3.5 S_central 1076 748 2207 2.751 0.789 0.137 0.054 16 2.1 S_cingul-Marginalis 620 402 1318 3.117 0.937 0.111 0.035 5 0.8 S_circular_insula_ant 1027 675 2056 3.308 0.850 0.080 0.020 4 0.8 S_circular_insula_inf 1613 1127 2644 2.419 0.769 0.107 0.027 11 1.9 S_circular_insula_sup 1233 893 2364 2.726 0.739 0.108 0.024 7 1.4 S_collat_transv_ant 533 363 778 2.604 0.558 0.127 0.037 4 0.9 S_collat_transv_post 1971 1344 2779 2.102 0.713 0.127 0.045 21 3.9 S_front_inf 1414 1028 2920 2.452 0.992 0.140 0.053 17 2.8 S_front_middle 2939 2031 4804 2.299 0.667 0.113 0.030 21 3.5 S_front_sup 265 182 458 2.704 0.538 0.106 0.026 1 0.3 S_interm_prim-Jensen 2254 1570 4056 2.719 0.746 0.131 0.044 23 3.9 S_intrapariet_and_P_trans 929 624 1585 2.509 0.761 0.162 0.087 17 3.6 S_oc_middle_and_Lunatus 1403 1026 2941 2.738 0.695 0.167 0.056 23 3.5 S_oc_sup_and_transversal 1179 833 2002 2.626 0.617 0.125 0.041 13 2.0 S_occipital_ant 881 580 1786 3.194 0.598 0.136 0.050 12 1.7 S_oc-temp_lat 1788 1233 2980 2.590 0.526 0.112 0.038 23 2.6 S_oc-temp_med_and_Lingual 443 313 593 1.731 0.730 0.130 0.034 3 0.7 S_orbital_lateral 787 589 1696 2.837 0.993 0.126 0.073 11 1.8 S_orbital_med-olfact 1545 1070 2660 2.335 0.657 0.152 0.064 47 4.1 S_orbital-H_Shaped 1467 1029 2143 2.292 0.736 0.189 0.095 33 5.3 S_parieto_occipital 1861 1203 2197 2.098 1.100 0.133 0.058 29 5.4 S_pericallosal 1523 1054 2649 2.332 0.800 0.134 0.051 58 3.4 S_postcentral 2438 1641 4820 2.588 0.747 0.122 0.038 31 4.0 S_precentral-inf-part 1901 1297 2694 2.250 0.598 0.126 0.040 17 3.1 S_precentral-sup-part 142 91 454 4.338 0.575 0.127 0.046 1 0.2 S_suborbital 2571 1704 5360 2.929 0.614 0.136 0.054 32 5.6 S_subparietal 1604 1117 2521 2.510 0.704 0.113 0.027 11 1.9 S_temporal_inf 8219 5609 15827 2.812 0.727 0.124 0.043 88 16.0 S_temporal_sup 393 280 690 2.766 0.818 0.110 0.026 2 0.5 S_temporal_transverse #-------------------------------------------- #@# Cortical ribbon mask Thu Aug 18 03:43:42 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance NF108_11 SUBJECTS_DIR is /export/data1/tools/freesurfer/subjects/hannahas 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 = 128 writing volume /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Thu Aug 18 03:58:54 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 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 /export/data1/tools/freesurfer/ASegStatsLUT.txt --subject NF108_11 $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 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 /export/data1/tools/freesurfer/ASegStatsLUT.txt --subject NF108_11 sysname Linux hostname localhost.localdomain machine x86_64 user hannahas atlas_icv (eTIV) = 1554700 mm^3 (det: 1.253042 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 213165 rh white matter volume 214163 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 236672.777174, pTot = 538375.708980 c = 301702.931806 rh surface-based volumes (mm3): wTot = 235097.757436, pTot = 533962.359233 c = 298864.601797 Computing SupraTentVolCor SupraTentVolCor = 72596.000 SupraTentVol = 1144934.068 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 5891 5891 4 5 Left-Inf-Lat-Vent 183 183 5 7 Left-Cerebellum-White-Matter 13615 13615 6 8 Left-Cerebellum-Cortex 60701 60701 7 10 Left-Thalamus-Proper 7877 7877 8 11 Left-Caudate 4854 4854 9 12 Left-Putamen 7012 7012 10 13 Left-Pallidum 2223 2223 11 14 3rd-Ventricle 753 753 12 15 4th-Ventricle 1793 1793 13 16 Brain-Stem 21064 21064 14 17 Left-Hippocampus 4424 4424 15 18 Left-Amygdala 1557 1557 16 24 CSF 1014 1014 17 26 Left-Accumbens-area 870 870 18 28 Left-VentralDC 4670 4670 19 30 Left-vessel 104 104 20 31 Left-choroid-plexus 1979 1979 23 43 Right-Lateral-Ventricle 4998 4998 24 44 Right-Inf-Lat-Vent 96 96 25 46 Right-Cerebellum-White-Matter 14868 14868 26 47 Right-Cerebellum-Cortex 62513 62513 27 49 Right-Thalamus-Proper 7910 7910 28 50 Right-Caudate 5120 5120 29 51 Right-Putamen 6659 6659 30 52 Right-Pallidum 2283 2283 31 53 Right-Hippocampus 4147 4147 32 54 Right-Amygdala 1622 1622 33 58 Right-Accumbens-area 724 724 34 60 Right-VentralDC 4349 4349 35 62 Right-vessel 75 75 36 63 Right-choroid-plexus 1903 1903 37 72 5th-Ventricle 22 22 38 77 WM-hypointensities 2025 2025 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 11 11 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 318 318 45 251 CC_Posterior 803 803 46 252 CC_Mid_Posterior 359 359 47 253 CC_Central 342 342 48 254 CC_Mid_Anterior 369 369 49 255 CC_Anterior 768 768 Reporting on 45 segmentations SubCortGrayVol = 210579 #----------------------------------------- #@# AParc-to-ASeg Thu Aug 18 04:07:39 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 mri_aparc2aseg --s NF108_11 --volmask SUBJECTS_DIR /export/data1/tools/freesurfer/subjects/hannahas subject NF108_11 outvol /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white Reading lh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial Loading lh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white Reading rh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial Loading rh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 = 590500 Used brute-force search on 0 voxels Writing output aseg to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aparc+aseg.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 mri_aparc2aseg --s NF108_11 --volmask --a2009s SUBJECTS_DIR /export/data1/tools/freesurfer/subjects/hannahas subject NF108_11 outvol /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white Reading lh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial Loading lh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white Reading rh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial Loading rh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 = 590500 Used brute-force search on 0 voxels Writing output aseg to /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Thu Aug 18 04:10:37 EDT 2011 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 mri_aparc2aseg --s NF108_11 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /export/data1/tools/freesurfer/subjects/hannahas subject NF108_11 outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aparc+aseg.mgz Reading lh white surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.white Reading lh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/lh.pial Loading lh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.white Reading rh pial surface /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/surf/rh.pial Loading rh annotations from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/ribbon.mgz Loading filled from /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/filled.mgz Ripping vertices labeled as unkown Ripped 7236 vertices from left hemi Ripped 7585 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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/mri/aseg.mgz Loading Ctx Seg File /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/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 = 987975 Used brute-force search on 17 voxels Fixing Parahip LH WM Found 14 clusters 0 k 5.000000 1 k 1.000000 2 k 1.000000 3 k 1.000000 4 k 2.000000 5 k 26.000000 6 k 12.000000 7 k 1.000000 8 k 2.000000 9 k 2.000000 10 k 1562.000000 11 k 3.000000 12 k 1.000000 13 k 1.000000 Fixing Parahip RH WM Found 9 clusters 0 k 2.000000 1 k 2.000000 2 k 1.000000 3 k 1261.000000 4 k 14.000000 5 k 2.000000 6 k 1.000000 7 k 43.000000 8 k 1.000000 Writing output aseg to mri/wmparc.mgz /export/data1/tools/freesurfer/subjects/hannahas/NF108_11 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 NF108_11 --surf-wm-vol --ctab /export/data1/tools/freesurfer/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 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 NF108_11 --surf-wm-vol --ctab /export/data1/tools/freesurfer/WMParcStatsLUT.txt --etiv sysname Linux hostname localhost.localdomain machine x86_64 user hannahas atlas_icv (eTIV) = 1554700 mm^3 (det: 1.253042 ) Loading mri/wmparc.mgz Getting Cerebral WM volumes from surface lh white matter volume 213165 rh white matter volume 214163 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1625269 # brainmaskvolume 1625269.0 # nbrainsegvoxels 258303 # brainsegvolume 258303.0 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 3035 3035 2 3002 wm-lh-caudalanteriorcingulate 3312 3312 3 3003 wm-lh-caudalmiddlefrontal 5720 5720 4 3004 wm-lh-corpuscallosum 0 5 3005 wm-lh-cuneus 2052 2052 6 3006 wm-lh-entorhinal 745 745 7 3007 wm-lh-fusiform 8051 8051 8 3008 wm-lh-inferiorparietal 10783 10783 9 3009 wm-lh-inferiortemporal 7143 7143 10 3010 wm-lh-isthmuscingulate 3189 3189 11 3011 wm-lh-lateraloccipital 9897 9897 12 3012 wm-lh-lateralorbitofrontal 5845 5845 13 3013 wm-lh-lingual 4924 4924 14 3014 wm-lh-medialorbitofrontal 3603 3603 15 3015 wm-lh-middletemporal 5340 5340 16 3016 wm-lh-parahippocampal 1760 1760 17 3017 wm-lh-paracentral 2778 2778 18 3018 wm-lh-parsopercularis 3377 3377 19 3019 wm-lh-parsorbitalis 795 795 20 3020 wm-lh-parstriangularis 2583 2583 21 3021 wm-lh-pericalcarine 2980 2980 22 3022 wm-lh-postcentral 6476 6476 23 3023 wm-lh-posteriorcingulate 3241 3241 24 3024 wm-lh-precentral 10300 10300 25 3025 wm-lh-precuneus 7978 7978 26 3026 wm-lh-rostralanteriorcingulate 2876 2876 27 3027 wm-lh-rostralmiddlefrontal 10755 10755 28 3028 wm-lh-superiorfrontal 14789 14789 29 3029 wm-lh-superiorparietal 10350 10350 30 3030 wm-lh-superiortemporal 5884 5884 31 3031 wm-lh-supramarginal 8636 8636 32 3032 wm-lh-frontalpole 349 349 33 3033 wm-lh-temporalpole 634 634 34 3034 wm-lh-transversetemporal 1043 1043 35 3035 wm-lh-insula 7854 7854 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 3107 3107 120 4002 wm-rh-caudalanteriorcingulate 2422 2422 121 4003 wm-rh-caudalmiddlefrontal 5458 5458 122 4004 wm-rh-corpuscallosum 0 123 4005 wm-rh-cuneus 1914 1914 124 4006 wm-rh-entorhinal 418 418 125 4007 wm-rh-fusiform 5672 5672 126 4008 wm-rh-inferiorparietal 13785 13785 127 4009 wm-rh-inferiortemporal 6110 6110 128 4010 wm-rh-isthmuscingulate 3234 3234 129 4011 wm-rh-lateraloccipital 7663 7663 130 4012 wm-rh-lateralorbitofrontal 5834 5834 131 4013 wm-rh-lingual 2994 2994 132 4014 wm-rh-medialorbitofrontal 3237 3237 133 4015 wm-rh-middletemporal 6398 6398 134 4016 wm-rh-parahippocampal 1411 1411 135 4017 wm-rh-paracentral 3216 3216 136 4018 wm-rh-parsopercularis 2759 2759 137 4019 wm-rh-parsorbitalis 988 988 138 4020 wm-rh-parstriangularis 3241 3241 139 4021 wm-rh-pericalcarine 1283 1283 140 4022 wm-rh-postcentral 5176 5176 141 4023 wm-rh-posteriorcingulate 4384 4384 142 4024 wm-rh-precentral 11011 11011 143 4025 wm-rh-precuneus 11490 11490 144 4026 wm-rh-rostralanteriorcingulate 2377 2377 145 4027 wm-rh-rostralmiddlefrontal 12286 12286 146 4028 wm-rh-superiorfrontal 17021 17021 147 4029 wm-rh-superiorparietal 11021 11021 148 4030 wm-rh-superiortemporal 5856 5856 149 4031 wm-rh-supramarginal 7311 7311 150 4032 wm-rh-frontalpole 642 642 151 4033 wm-rh-temporalpole 537 537 152 4034 wm-rh-transversetemporal 615 615 153 4035 wm-rh-insula 8476 8476 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 20998 20998 237 5002 Right-UnsegmentedWhiteMatter 20706 20706 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 /export/data1/tools/freesurfer/subjects/hannahas/NF108_11/label #-------------------------------------------- #@# BA Labels lh Thu Aug 18 04:27:25 EDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... ln -s /export/data1/tools/freesurfer/subjects/fsaverage /export/data1/tools/freesurfer/subjects/hannahas/fsaverage ln: creating symbolic link `/export/data1/tools/freesurfer/subjects/hannahas/fsaverage': File exists mri_label2label --srcsubject fsaverage --srclabel /export/data1/tools/freesurfer/subjects/hannahas/fsaverage/label/lh.BA1.label --trgsubject NF108_11 --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /export/data1/tools/freesurfer/subjects/hannahas/fsaverage/label/lh.BA1.label srclabel = /export/data1/tools/freesurfer/subjects/hannahas/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = NF108_11 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 /export/data1/tools/freesurfer/subjects/hannahas FREESURFER_HOME /export/data1/tools/freesurfer Loading source label. Invalid argument ERROR reading /export/data1/tools/freesurfer/subjects/hannahas/fsaverage/label/lh.BA1.label Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NF108_11 exited with ERRORS at Thu Aug 18 04:27:25 EDT 2011 New invocation of recon-all Mon Apr 30 18:35:54 EDT 2012 /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11 /export/data1/tools/freesurfer/bin/recon-all -s NF108_11 -autorecon2-cp -autorecon3 subjid NF108_11 setenv SUBJECTS_DIR /export/data2/data1/tools/freesurfer/subjects/soo-eun FREESURFER_HOME /export/data1/tools/freesurfer Actual FREESURFER_HOME /export/data2/data1/tools/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16334248 14136844 2197404 0 13124 124128 -/+ buffers/cache: 13999592 2334656 Swap: 18579448 14224556 4354892 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:54-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:55-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:56-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:57-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/30-22:35:58-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /export/data1/tools/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /export/data1/tools/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Intensity Normalization2 Mon Apr 30 18:35:58 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/mri mri_normalize -f /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/tmp/control.dat -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using control points from file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/tmp/control.dat... using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... Reading 80 control points... only using 80 control points from file, mean 85.4, scaling by 1.29... building Voronoi diagram... performing soap bubble smoothing... removing outliers in the aseg WM... 5680 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 4 minutes and 12 seconds. using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 108 gm peak at 65 (65), valley at 0 (-1) csf peak at 32, setting threshold to 54 white matter peak found at 111 white matter peak found at 110 gm peak at 65 (65), valley at 0 (-1) csf peak at 32, setting threshold to 54 #-------------------------------------------- #@# Mask BFS Mon Apr 30 18:40:12 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1621136 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Apr 30 18:40:15 EDT 2012 cp wm.mgz wm.seg.mgz mri_segment -keep brain.mgz wm.seg.mgz preserving editing changes in output volume... doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.7 +- 5.9 [80.0 --> 125.0] GM (71.0) : 69.7 +- 9.2 [30.0 --> 96.0] setting bottom of white matter range to 78.9 setting top of gray matter range to 88.1 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... 10221 sparsely connected voxels removed... thickening thin strands.... 20 segments, 5422 filled 15 bright non-wm voxels segmented. 4258 diagonally connected voxels added... white matter segmentation took 1.0 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 0.70 minutes reading wm segmentation from wm.seg.mgz... 782 voxels added to wm to prevent paths from MTL structures to cortex 1440 additional wm voxels added 0 additional wm voxels added SEG EDIT: 50801 voxels turned on, 33162 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 -keep wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 29 found - 29 modified | TOTAL: 29 pass 2 (xy+): 0 found - 29 modified | TOTAL: 29 pass 1 (xy-): 30 found - 30 modified | TOTAL: 59 pass 2 (xy-): 0 found - 30 modified | TOTAL: 59 pass 1 (yz+): 30 found - 30 modified | TOTAL: 89 pass 2 (yz+): 0 found - 30 modified | TOTAL: 89 pass 1 (yz-): 23 found - 23 modified | TOTAL: 112 pass 2 (yz-): 0 found - 23 modified | TOTAL: 112 pass 1 (xz+): 28 found - 28 modified | TOTAL: 140 pass 2 (xz+): 0 found - 28 modified | TOTAL: 140 pass 1 (xz-): 17 found - 17 modified | TOTAL: 157 pass 2 (xz-): 0 found - 17 modified | TOTAL: 157 Iteration Number : 1 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 23 found - 23 modified | TOTAL: 43 pass 2 (+++): 0 found - 23 modified | TOTAL: 43 pass 1 (+++): 24 found - 24 modified | TOTAL: 67 pass 2 (+++): 0 found - 24 modified | TOTAL: 67 pass 1 (+++): 33 found - 33 modified | TOTAL: 100 pass 2 (+++): 0 found - 33 modified | TOTAL: 100 Iteration Number : 1 pass 1 (++): 212 found - 212 modified | TOTAL: 212 pass 2 (++): 0 found - 212 modified | TOTAL: 212 pass 1 (+-): 198 found - 198 modified | TOTAL: 410 pass 2 (+-): 0 found - 198 modified | TOTAL: 410 pass 1 (--): 170 found - 170 modified | TOTAL: 580 pass 2 (--): 0 found - 170 modified | TOTAL: 580 pass 1 (-+): 212 found - 212 modified | TOTAL: 792 pass 2 (-+): 0 found - 212 modified | TOTAL: 792 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 10 found - 10 modified | TOTAL: 13 pass 2 (xy-): 0 found - 10 modified | TOTAL: 13 pass 1 (yz+): 5 found - 5 modified | TOTAL: 18 pass 2 (yz+): 0 found - 5 modified | TOTAL: 18 pass 1 (yz-): 13 found - 13 modified | TOTAL: 31 pass 2 (yz-): 0 found - 13 modified | TOTAL: 31 pass 1 (xz+): 7 found - 7 modified | TOTAL: 38 pass 2 (xz+): 0 found - 7 modified | TOTAL: 38 pass 1 (xz-): 12 found - 12 modified | TOTAL: 50 pass 2 (xz-): 0 found - 12 modified | TOTAL: 50 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 3 found - 3 modified | TOTAL: 11 pass 2 (+-): 0 found - 3 modified | TOTAL: 11 pass 1 (--): 6 found - 6 modified | TOTAL: 17 pass 2 (--): 0 found - 6 modified | TOTAL: 17 pass 1 (-+): 0 found - 0 modified | TOTAL: 17 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 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 = 1120 (out of 504622: 0.221948) keeping edits binarizing input wm segmentation... Ambiguous edge configurations... Searching for edits to keep ... kept 0 WM ON voxels kept 0 WM OFF voxels mri_pretess done #-------------------------------------------- #@# Fill Mon Apr 30 18:42:03 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.174 -0.043 0.082 -30.901; 0.027 1.089 0.310 -29.148; -0.081 -0.266 0.941 43.314; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2501 (min = 350, max = 1400), aspect = 1.29 (min = 0.10, max = 0.75) need search nearby using seed (126, 113, 89), TAL = (2.0, -39.0, 15.0) talairach voxel to voxel transform 0.846 0.014 -0.078 29.936; -0.039 0.849 -0.276 35.505; 0.062 0.242 0.978 -33.400; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 113, 89) --> (2.0, -39.0, 15.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (2.00, -39.00, 15.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -39.00, 15.00) SRC: (115.91, 102.69, 87.63) search lh wm seed point around talairach space (-16.00, -39.00, 15.00), SRC: (146.36, 101.29, 89.86) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Mon Apr 30 18:42:52 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 6 found - 6 modified | TOTAL: 9 pass 2 (yz+): 0 found - 6 modified | TOTAL: 9 pass 1 (yz-): 1 found - 1 modified | TOTAL: 10 pass 2 (yz-): 0 found - 1 modified | TOTAL: 10 pass 1 (xz+): 4 found - 4 modified | TOTAL: 14 pass 2 (xz+): 0 found - 4 modified | TOTAL: 14 pass 1 (xz-): 1 found - 1 modified | TOTAL: 15 pass 2 (xz-): 0 found - 1 modified | TOTAL: 15 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 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 : 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 Iteration Number : 3 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 : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 18 (out of 243728: 0.007385) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ slice 30: 156 vertices, 189 faces slice 40: 4837 vertices, 5029 faces slice 50: 12280 vertices, 12563 faces slice 60: 21199 vertices, 21548 faces slice 70: 31126 vertices, 31561 faces slice 80: 41964 vertices, 42386 faces slice 90: 52630 vertices, 53082 faces slice 100: 64684 vertices, 65218 faces slice 110: 76562 vertices, 77030 faces slice 120: 88275 vertices, 88799 faces slice 130: 99703 vertices, 100242 faces slice 140: 110694 vertices, 111219 faces slice 150: 121102 vertices, 121596 faces slice 160: 129422 vertices, 129835 faces slice 170: 136021 vertices, 136391 faces slice 180: 141630 vertices, 141955 faces slice 190: 146511 vertices, 146855 faces slice 200: 149424 vertices, 149610 faces slice 210: 149424 vertices, 149610 faces slice 220: 149424 vertices, 149610 faces slice 230: 149424 vertices, 149610 faces slice 240: 149424 vertices, 149610 faces slice 250: 149424 vertices, 149610 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... 149424 voxel in cpt #1: X=-186 [v=149424,e=448830,f=299220] located at (-29.543568, -19.633633, 32.110256) For the whole surface: X=-186 [v=149424,e=448830,f=299220] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Mon Apr 30 18:43:03 EDT 2012 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Mon Apr 30 18:43:08 EDT 2012 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts avg radius = 48.3 mm, total surface area = 76722 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.0 minutes Not saving sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.073 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.051 (target=0.015) step 040: RMS=0.049 (target=0.015) step 045: RMS=0.048 (target=0.015) step 050: RMS=0.047 (target=0.015) step 055: RMS=0.047 (target=0.015) step 060: RMS=0.046 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Mon Apr 30 18:44:09 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.62 (0.00-->7.10) (max @ vno 63110 --> 64379) face area 0.02 +- 0.03 (-0.17-->0.66) scaling brain by 0.286... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.822, avgs=0 005/300: dt: 0.9000, rms radial error=177.563, avgs=0 010/300: dt: 0.9000, rms radial error=177.006, avgs=0 015/300: dt: 0.9000, rms radial error=176.275, avgs=0 020/300: dt: 0.9000, rms radial error=175.440, avgs=0 025/300: dt: 0.9000, rms radial error=174.545, avgs=0 030/300: dt: 0.9000, rms radial error=173.620, avgs=0 035/300: dt: 0.9000, rms radial error=172.677, avgs=0 040/300: dt: 0.9000, rms radial error=171.727, avgs=0 045/300: dt: 0.9000, rms radial error=170.774, avgs=0 050/300: dt: 0.9000, rms radial error=169.824, avgs=0 055/300: dt: 0.9000, rms radial error=168.876, avgs=0 060/300: dt: 0.9000, rms radial error=167.932, avgs=0 065/300: dt: 0.9000, rms radial error=166.992, avgs=0 070/300: dt: 0.9000, rms radial error=166.057, avgs=0 075/300: dt: 0.9000, rms radial error=165.126, avgs=0 080/300: dt: 0.9000, rms radial error=164.200, avgs=0 085/300: dt: 0.9000, rms radial error=163.278, avgs=0 090/300: dt: 0.9000, rms radial error=162.362, avgs=0 095/300: dt: 0.9000, rms radial error=161.449, avgs=0 100/300: dt: 0.9000, rms radial error=160.542, avgs=0 105/300: dt: 0.9000, rms radial error=159.640, avgs=0 110/300: dt: 0.9000, rms radial error=158.742, avgs=0 115/300: dt: 0.9000, rms radial error=157.849, avgs=0 120/300: dt: 0.9000, rms radial error=156.961, avgs=0 125/300: dt: 0.9000, rms radial error=156.078, avgs=0 130/300: dt: 0.9000, rms radial error=155.199, avgs=0 135/300: dt: 0.9000, rms radial error=154.325, avgs=0 140/300: dt: 0.9000, rms radial error=153.456, avgs=0 145/300: dt: 0.9000, rms radial error=152.591, avgs=0 150/300: dt: 0.9000, rms radial error=151.731, avgs=0 155/300: dt: 0.9000, rms radial error=150.876, avgs=0 160/300: dt: 0.9000, rms radial error=150.025, avgs=0 165/300: dt: 0.9000, rms radial error=149.179, avgs=0 170/300: dt: 0.9000, rms radial error=148.337, avgs=0 175/300: dt: 0.9000, rms radial error=147.500, avgs=0 180/300: dt: 0.9000, rms radial error=146.667, avgs=0 185/300: dt: 0.9000, rms radial error=145.838, avgs=0 190/300: dt: 0.9000, rms radial error=145.015, avgs=0 195/300: dt: 0.9000, rms radial error=144.197, avgs=0 200/300: dt: 0.9000, rms radial error=143.383, avgs=0 205/300: dt: 0.9000, rms radial error=142.574, avgs=0 210/300: dt: 0.9000, rms radial error=141.769, avgs=0 215/300: dt: 0.9000, rms radial error=140.968, avgs=0 220/300: dt: 0.9000, rms radial error=140.172, avgs=0 225/300: dt: 0.9000, rms radial error=139.380, avgs=0 230/300: dt: 0.9000, rms radial error=138.592, avgs=0 235/300: dt: 0.9000, rms radial error=137.809, avgs=0 240/300: dt: 0.9000, rms radial error=137.031, avgs=0 245/300: dt: 0.9000, rms radial error=136.257, avgs=0 250/300: dt: 0.9000, rms radial error=135.487, avgs=0 255/300: dt: 0.9000, rms radial error=134.722, avgs=0 260/300: dt: 0.9000, rms radial error=133.961, avgs=0 265/300: dt: 0.9000, rms radial error=133.204, avgs=0 270/300: dt: 0.9000, rms radial error=132.452, avgs=0 275/300: dt: 0.9000, rms radial error=131.704, avgs=0 280/300: dt: 0.9000, rms radial error=130.960, avgs=0 285/300: dt: 0.9000, rms radial error=130.220, avgs=0 290/300: dt: 0.9000, rms radial error=129.485, avgs=0 295/300: dt: 0.9000, rms radial error=128.753, avgs=0 300/300: dt: 0.9000, rms radial error=128.026, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 7996.80 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00006 epoch 2 (K=80.0), pass 1, starting sse = 1224.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00047 epoch 3 (K=320.0), pass 1, starting sse = 139.91 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00453 epoch 4 (K=1280.0), pass 1, starting sse = 18.26 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/11 = 0.00463 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Mon Apr 30 18:50:01 EDT 2012 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 NF108_11 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 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-186 (nv=149424, nf=299220, ne=448830, g=94) 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 12 iterations marking ambiguous vertices... 18875 ambiguous faces found in tessellation segmenting defects... 102 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 0 into 2 -merging segment 37 into 32 100 defects to be corrected 0 vertices coincident reading input surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5166 (-4.7583) -vertex loglikelihood: -6.4021 (-3.2011) -normal dot loglikelihood: -3.6076 (-3.6076) -quad curv loglikelihood: -6.3972 (-3.1986) Total Loglikelihood : -25.9236 CORRECTING DEFECT 0 (vertices=41, convex hull=70) After retessellation of defect 0, euler #=-99 (138247,410957,272611) : difference with theory (-97) = 2 CORRECTING DEFECT 1 (vertices=1071, convex hull=502) After retessellation of defect 1, euler #=-97 (138431,411741,273213) : difference with theory (-96) = 1 CORRECTING DEFECT 2 (vertices=24, convex hull=57) After retessellation of defect 2, euler #=-96 (138437,411783,273250) : difference with theory (-95) = 1 CORRECTING DEFECT 3 (vertices=36, convex hull=47) After retessellation of defect 3, euler #=-95 (138448,411838,273295) : difference with theory (-94) = 1 CORRECTING DEFECT 4 (vertices=105, convex hull=147) After retessellation of defect 4, euler #=-94 (138509,412087,273484) : difference with theory (-93) = 1 CORRECTING DEFECT 5 (vertices=14, convex hull=27) After retessellation of defect 5, euler #=-93 (138512,412106,273501) : difference with theory (-92) = 1 CORRECTING DEFECT 6 (vertices=30, convex hull=58) After retessellation of defect 6, euler #=-92 (138527,412173,273554) : difference with theory (-91) = 1 CORRECTING DEFECT 7 (vertices=218, convex hull=131) After retessellation of defect 7, euler #=-91 (138571,412369,273707) : difference with theory (-90) = 1 CORRECTING DEFECT 8 (vertices=117, convex hull=126) After retessellation of defect 8, euler #=-90 (138597,412502,273815) : difference with theory (-89) = 1 CORRECTING DEFECT 9 (vertices=125, convex hull=66) After retessellation of defect 9, euler #=-89 (138616,412585,273880) : difference with theory (-88) = 1 CORRECTING DEFECT 10 (vertices=67, convex hull=54) After retessellation of defect 10, euler #=-88 (138622,412623,273913) : difference with theory (-87) = 1 CORRECTING DEFECT 11 (vertices=45, convex hull=82) After retessellation of defect 11, euler #=-87 (138644,412724,273993) : difference with theory (-86) = 1 CORRECTING DEFECT 12 (vertices=82, convex hull=137) After retessellation of defect 12, euler #=-86 (138686,412908,274136) : difference with theory (-85) = 1 CORRECTING DEFECT 13 (vertices=229, convex hull=167) After retessellation of defect 13, euler #=-85 (138739,413142,274318) : difference with theory (-84) = 1 CORRECTING DEFECT 14 (vertices=60, convex hull=38) After retessellation of defect 14, euler #=-84 (138740,413161,274337) : difference with theory (-83) = 1 CORRECTING DEFECT 15 (vertices=13, convex hull=24) After retessellation of defect 15, euler #=-83 (138740,413170,274347) : difference with theory (-82) = 1 CORRECTING DEFECT 16 (vertices=21, convex hull=31) After retessellation of defect 16, euler #=-82 (138743,413190,274365) : difference with theory (-81) = 1 CORRECTING DEFECT 17 (vertices=5, convex hull=27) After retessellation of defect 17, euler #=-81 (138744,413200,274375) : difference with theory (-80) = 1 CORRECTING DEFECT 18 (vertices=51, convex hull=83) After retessellation of defect 18, euler #=-80 (138755,413267,274432) : difference with theory (-79) = 1 CORRECTING DEFECT 19 (vertices=27, convex hull=41) After retessellation of defect 19, euler #=-79 (138756,413282,274447) : difference with theory (-78) = 1 CORRECTING DEFECT 20 (vertices=24, convex hull=28) After retessellation of defect 20, euler #=-78 (138758,413298,274462) : difference with theory (-77) = 1 CORRECTING DEFECT 21 (vertices=118, convex hull=176) After retessellation of defect 21, euler #=-77 (138826,413583,274680) : difference with theory (-76) = 1 CORRECTING DEFECT 22 (vertices=77, convex hull=34) After retessellation of defect 22, euler #=-76 (138834,413620,274710) : difference with theory (-75) = 1 CORRECTING DEFECT 23 (vertices=26, convex hull=18) After retessellation of defect 23, euler #=-75 (138834,413625,274716) : difference with theory (-74) = 1 CORRECTING DEFECT 24 (vertices=37, convex hull=83) After retessellation of defect 24, euler #=-74 (138850,413707,274783) : difference with theory (-73) = 1 CORRECTING DEFECT 25 (vertices=583, convex hull=155) After retessellation of defect 25, euler #=-73 (138920,414002,275009) : difference with theory (-72) = 1 CORRECTING DEFECT 26 (vertices=32, convex hull=43) After retessellation of defect 26, euler #=-72 (138923,414030,275035) : difference with theory (-71) = 1 CORRECTING DEFECT 27 (vertices=75, convex hull=65) After retessellation of defect 27, euler #=-71 (138939,414104,275094) : difference with theory (-70) = 1 CORRECTING DEFECT 28 (vertices=67, convex hull=114) After retessellation of defect 28, euler #=-70 (138972,414252,275210) : difference with theory (-69) = 1 CORRECTING DEFECT 29 (vertices=31, convex hull=39) After retessellation of defect 29, euler #=-69 (138974,414274,275231) : difference with theory (-68) = 1 CORRECTING DEFECT 30 (vertices=72, convex hull=126) After retessellation of defect 30, euler #=-68 (139008,414431,275355) : difference with theory (-67) = 1 CORRECTING DEFECT 31 (vertices=209, convex hull=187) After retessellation of defect 31, euler #=-66 (139094,414777,275617) : difference with theory (-66) = 0 CORRECTING DEFECT 32 (vertices=112, convex hull=130) After retessellation of defect 32, euler #=-65 (139156,415021,275800) : difference with theory (-65) = 0 CORRECTING DEFECT 33 (vertices=21, convex hull=41) After retessellation of defect 33, euler #=-64 (139160,415045,275821) : difference with theory (-64) = 0 CORRECTING DEFECT 34 (vertices=29, convex hull=35) After retessellation of defect 34, euler #=-63 (139165,415072,275844) : difference with theory (-63) = 0 CORRECTING DEFECT 35 (vertices=117, convex hull=186) After retessellation of defect 35, euler #=-62 (139223,415330,276045) : difference with theory (-62) = 0 CORRECTING DEFECT 36 (vertices=81, convex hull=68) After retessellation of defect 36, euler #=-61 (139243,415415,276111) : difference with theory (-61) = 0 CORRECTING DEFECT 37 (vertices=24, convex hull=58) After retessellation of defect 37, euler #=-60 (139252,415465,276153) : difference with theory (-60) = 0 CORRECTING DEFECT 38 (vertices=53, convex hull=88) After retessellation of defect 38, euler #=-59 (139276,415573,276238) : difference with theory (-59) = 0 CORRECTING DEFECT 39 (vertices=60, convex hull=97) After retessellation of defect 39, euler #=-58 (139305,415701,276338) : difference with theory (-58) = 0 CORRECTING DEFECT 40 (vertices=23, convex hull=31) After retessellation of defect 40, euler #=-57 (139307,415719,276355) : difference with theory (-57) = 0 CORRECTING DEFECT 41 (vertices=94, convex hull=106) After retessellation of defect 41, euler #=-56 (139356,415913,276501) : difference with theory (-56) = 0 CORRECTING DEFECT 42 (vertices=41, convex hull=81) After retessellation of defect 42, euler #=-55 (139377,416010,276578) : difference with theory (-55) = 0 CORRECTING DEFECT 43 (vertices=31, convex hull=90) After retessellation of defect 43, euler #=-54 (139392,416088,276642) : difference with theory (-54) = 0 CORRECTING DEFECT 44 (vertices=266, convex hull=83) After retessellation of defect 44, euler #=-53 (139402,416157,276702) : difference with theory (-53) = 0 CORRECTING DEFECT 45 (vertices=50, convex hull=109) After retessellation of defect 45, euler #=-52 (139415,416236,276769) : difference with theory (-52) = 0 CORRECTING DEFECT 46 (vertices=13, convex hull=25) After retessellation of defect 46, euler #=-51 (139416,416248,276781) : difference with theory (-51) = 0 CORRECTING DEFECT 47 (vertices=537, convex hull=386) After retessellation of defect 47, euler #=-50 (139570,416909,277289) : difference with theory (-50) = 0 CORRECTING DEFECT 48 (vertices=75, convex hull=103) After retessellation of defect 48, euler #=-49 (139609,417072,277414) : difference with theory (-49) = 0 CORRECTING DEFECT 49 (vertices=7, convex hull=29) After retessellation of defect 49, euler #=-48 (139610,417087,277429) : difference with theory (-48) = 0 CORRECTING DEFECT 50 (vertices=75, convex hull=82) After retessellation of defect 50, euler #=-47 (139638,417204,277519) : difference with theory (-47) = 0 CORRECTING DEFECT 51 (vertices=13, convex hull=22) After retessellation of defect 51, euler #=-46 (139641,417218,277531) : difference with theory (-46) = 0 CORRECTING DEFECT 52 (vertices=55, convex hull=52) After retessellation of defect 52, euler #=-45 (139660,417298,277593) : difference with theory (-45) = 0 CORRECTING DEFECT 53 (vertices=165, convex hull=137) After retessellation of defect 53, euler #=-44 (139726,417560,277790) : difference with theory (-44) = 0 CORRECTING DEFECT 54 (vertices=453, convex hull=205) After retessellation of defect 54, euler #=-43 (139779,417828,278006) : difference with theory (-43) = 0 CORRECTING DEFECT 55 (vertices=32, convex hull=46) After retessellation of defect 55, euler #=-42 (139790,417878,278046) : difference with theory (-42) = 0 CORRECTING DEFECT 56 (vertices=263, convex hull=286) After retessellation of defect 56, euler #=-41 (139881,418287,278365) : difference with theory (-41) = 0 CORRECTING DEFECT 57 (vertices=50, convex hull=50) After retessellation of defect 57, euler #=-40 (139890,418332,278402) : difference with theory (-40) = 0 CORRECTING DEFECT 58 (vertices=350, convex hull=80) After retessellation of defect 58, euler #=-39 (139953,418556,278564) : difference with theory (-39) = 0 CORRECTING DEFECT 59 (vertices=42, convex hull=25) After retessellation of defect 59, euler #=-38 (139958,418580,278584) : difference with theory (-38) = 0 CORRECTING DEFECT 60 (vertices=54, convex hull=37) After retessellation of defect 60, euler #=-37 (139962,418604,278605) : difference with theory (-37) = 0 CORRECTING DEFECT 61 (vertices=60, convex hull=77) After retessellation of defect 61, euler #=-36 (139971,418660,278653) : difference with theory (-36) = 0 CORRECTING DEFECT 62 (vertices=6, convex hull=9) After retessellation of defect 62, euler #=-35 (139971,418662,278656) : difference with theory (-35) = 0 CORRECTING DEFECT 63 (vertices=123, convex hull=103) After retessellation of defect 63, euler #=-34 (140023,418866,278809) : difference with theory (-34) = 0 CORRECTING DEFECT 64 (vertices=28, convex hull=64) After retessellation of defect 64, euler #=-33 (140032,418914,278849) : difference with theory (-33) = 0 CORRECTING DEFECT 65 (vertices=717, convex hull=160) After retessellation of defect 65, euler #=-32 (140168,419407,279207) : difference with theory (-32) = 0 CORRECTING DEFECT 66 (vertices=64, convex hull=108) After retessellation of defect 66, euler #=-31 (140204,419557,279322) : difference with theory (-31) = 0 CORRECTING DEFECT 67 (vertices=194, convex hull=185) After retessellation of defect 67, euler #=-30 (140276,419864,279558) : difference with theory (-30) = 0 CORRECTING DEFECT 68 (vertices=26, convex hull=37) After retessellation of defect 68, euler #=-29 (140282,419893,279582) : difference with theory (-29) = 0 CORRECTING DEFECT 69 (vertices=9, convex hull=45) After retessellation of defect 69, euler #=-28 (140285,419917,279604) : difference with theory (-28) = 0 CORRECTING DEFECT 70 (vertices=21, convex hull=60) After retessellation of defect 70, euler #=-27 (140297,419971,279647) : difference with theory (-27) = 0 CORRECTING DEFECT 71 (vertices=66, convex hull=35) After retessellation of defect 71, euler #=-26 (140305,420009,279678) : difference with theory (-26) = 0 CORRECTING DEFECT 72 (vertices=28, convex hull=69) After retessellation of defect 72, euler #=-25 (140323,420089,279741) : difference with theory (-25) = 0 CORRECTING DEFECT 73 (vertices=67, convex hull=49) After retessellation of defect 73, euler #=-24 (140332,420137,279781) : difference with theory (-24) = 0 CORRECTING DEFECT 74 (vertices=37, convex hull=70) After retessellation of defect 74, euler #=-23 (140350,420217,279844) : difference with theory (-23) = 0 CORRECTING DEFECT 75 (vertices=94, convex hull=43) After retessellation of defect 75, euler #=-22 (140356,420255,279877) : difference with theory (-22) = 0 CORRECTING DEFECT 76 (vertices=58, convex hull=65) After retessellation of defect 76, euler #=-21 (140370,420320,279929) : difference with theory (-21) = 0 CORRECTING DEFECT 77 (vertices=381, convex hull=92) After retessellation of defect 77, euler #=-20 (140424,420527,280083) : difference with theory (-20) = 0 CORRECTING DEFECT 78 (vertices=122, convex hull=89) After retessellation of defect 78, euler #=-19 (140458,420667,280190) : difference with theory (-19) = 0 CORRECTING DEFECT 79 (vertices=11, convex hull=30) After retessellation of defect 79, euler #=-18 (140461,420686,280207) : difference with theory (-18) = 0 CORRECTING DEFECT 80 (vertices=22, convex hull=51) After retessellation of defect 80, euler #=-17 (140469,420731,280245) : difference with theory (-17) = 0 CORRECTING DEFECT 81 (vertices=95, convex hull=38) After retessellation of defect 81, euler #=-16 (140475,420764,280273) : difference with theory (-16) = 0 CORRECTING DEFECT 82 (vertices=89, convex hull=96) After retessellation of defect 82, euler #=-15 (140505,420896,280376) : difference with theory (-15) = 0 CORRECTING DEFECT 83 (vertices=486, convex hull=158) After retessellation of defect 83, euler #=-14 (140585,421219,280620) : difference with theory (-14) = 0 CORRECTING DEFECT 84 (vertices=7, convex hull=32) After retessellation of defect 84, euler #=-13 (140586,421230,280631) : difference with theory (-13) = 0 CORRECTING DEFECT 85 (vertices=28, convex hull=73) After retessellation of defect 85, euler #=-12 (140603,421311,280696) : difference with theory (-12) = 0 CORRECTING DEFECT 86 (vertices=69, convex hull=28) After retessellation of defect 86, euler #=-11 (140605,421325,280709) : difference with theory (-11) = 0 CORRECTING DEFECT 87 (vertices=156, convex hull=49) After retessellation of defect 87, euler #=-10 (140615,421377,280752) : difference with theory (-10) = 0 CORRECTING DEFECT 88 (vertices=315, convex hull=183) After retessellation of defect 88, euler #=-9 (140679,421654,280966) : difference with theory (-9) = 0 CORRECTING DEFECT 89 (vertices=42, convex hull=83) After retessellation of defect 89, euler #=-8 (140696,421740,281036) : difference with theory (-8) = 0 CORRECTING DEFECT 90 (vertices=78, convex hull=83) After retessellation of defect 90, euler #=-7 (140714,421836,281115) : difference with theory (-7) = 0 CORRECTING DEFECT 91 (vertices=63, convex hull=29) After retessellation of defect 91, euler #=-6 (140717,421854,281131) : difference with theory (-6) = 0 CORRECTING DEFECT 92 (vertices=200, convex hull=162) After retessellation of defect 92, euler #=-5 (140784,422129,281340) : difference with theory (-5) = 0 CORRECTING DEFECT 93 (vertices=201, convex hull=185) After retessellation of defect 93, euler #=-4 (140858,422438,281576) : difference with theory (-4) = 0 CORRECTING DEFECT 94 (vertices=134, convex hull=104) After retessellation of defect 94, euler #=-3 (140885,422561,281673) : difference with theory (-3) = 0 CORRECTING DEFECT 95 (vertices=58, convex hull=66) After retessellation of defect 95, euler #=-2 (140890,422604,281712) : difference with theory (-2) = 0 CORRECTING DEFECT 96 (vertices=8, convex hull=23) After retessellation of defect 96, euler #=-1 (140892,422616,281723) : difference with theory (-1) = 0 CORRECTING DEFECT 97 (vertices=42, convex hull=73) After retessellation of defect 97, euler #=0 (140901,422674,281773) : difference with theory (0) = 0 CORRECTING DEFECT 98 (vertices=36, convex hull=46) After retessellation of defect 98, euler #=1 (140903,422696,281794) : difference with theory (1) = 0 CORRECTING DEFECT 99 (vertices=25, convex hull=25) After retessellation of defect 99, euler #=2 (140905,422709,281806) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.06-->10.70) (max @ vno 103202 --> 105346) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.06-->10.70) (max @ vno 103202 --> 105346) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 356 mutations (36.2%), 628 crossovers (63.8%), 331 vertices were eliminated building final representation... 8519 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=140905, nf=281806, ne=422709, g=0) writing corrected surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 75.5 minutes 0 defective edges removing intersecting faces 000: 783 intersecting 001: 40 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 140905 - 422709 + 281806 = 2 --> 0 holes F =2V-4: 281806 = 281810-4 (0) 2E=3F: 845418 = 845418 (0) total defect index = 0 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 182 intersecting 001: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make Final Surf lh Mon Apr 30 20:05:42 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs NF108_11 lh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/filled.mgz... reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/brain.finalsurfs.mgz... reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/wm.mgz... 25122 bright wm thresholded. 33 bright non-wm voxels segmented. reading original surface position from /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.orig... computing class statistics... border white: 252008 voxels (1.50%) border gray 311945 voxels (1.86%) WM (96.0): 96.6 +- 8.9 [70.0 --> 110.0] GM (70.0) : 70.2 +- 9.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 57.3 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 67.0 (was 85) setting MAX_CSF to 47.5 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 62.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.24 (0.02-->4.92) (max @ vno 139805 --> 139824) face area 0.28 +- 0.13 (0.00-->4.08) mean absolute distance = 0.63 +- 0.76 4308 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=67 using class modes intead of means.... mean inside = 92.3, mean outside = 74.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=78.7, 165 (165) missing vertices, mean dist 0.3 [0.5 (%35.2)->0.7 (%64.8))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.28 (0.09-->5.15) (max @ vno 102958 --> 139883) face area 0.28 +- 0.14 (0.00-->4.20) mean absolute distance = 0.32 +- 0.51 3389 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5337580.0, rms=9.59 001: dt: 0.5000, sse=6479043.0, rms=6.83 002: dt: 0.5000, sse=7158327.5, rms=5.51 003: dt: 0.5000, sse=7597364.0, rms=4.84 004: dt: 0.5000, sse=7860083.0, rms=4.42 005: dt: 0.5000, sse=8007148.0, rms=4.20 006: dt: 0.5000, sse=8121845.5, rms=4.03 007: dt: 0.5000, sse=8136999.0, rms=3.96 008: dt: 0.5000, sse=8199439.0, rms=3.84 rms = 3.83, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=8168557.5, rms=3.83 010: dt: 0.2500, sse=5401212.5, rms=2.84 011: dt: 0.2500, sse=5010914.5, rms=2.58 012: dt: 0.2500, sse=4797307.0, rms=2.51 rms = 2.47, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=4740052.5, rms=2.47 014: dt: 0.1250, sse=4636488.0, rms=2.41 rms = 2.39, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=4605966.5, rms=2.39 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.7, 238 (50) missing vertices, mean dist -0.2 [0.3 (%72.9)->0.3 (%27.1))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.27 (0.05-->5.36) (max @ vno 96388 --> 96387) face area 0.34 +- 0.17 (0.00-->5.13) mean absolute distance = 0.25 +- 0.40 3144 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5097764.5, rms=4.39 016: dt: 0.5000, sse=5777241.5, rms=3.04 rms = 3.36, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=5374453.5, rms=2.39 018: dt: 0.2500, sse=5217930.0, rms=2.09 019: dt: 0.2500, sse=5137096.5, rms=1.98 rms = 1.96, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5079193.5, rms=1.96 021: dt: 0.1250, sse=5004512.0, rms=1.91 rms = 1.89, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4972122.5, rms=1.89 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=83.4, 235 (32) missing vertices, mean dist -0.1 [0.3 (%63.7)->0.3 (%36.3))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.05-->5.49) (max @ vno 96388 --> 96387) face area 0.34 +- 0.17 (0.00-->4.91) mean absolute distance = 0.24 +- 0.36 3303 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5068703.0, rms=2.75 rms = 2.85, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=5048475.5, rms=2.13 024: dt: 0.2500, sse=5131384.0, rms=1.79 rms = 1.75, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=5206612.0, rms=1.75 rms = 1.71, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=5128128.0, rms=1.71 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=84.0, 241 (23) missing vertices, mean dist -0.0 [0.2 (%53.3)->0.2 (%46.7))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5136511.0, rms=1.85 rms = 1.96, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5313532.0, rms=1.52 028: dt: 0.2500, sse=5664879.0, rms=1.37 rms = 1.39, time step reduction 2 of 3 to 0.125... rms = 1.37, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5669890.5, rms=1.37 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... label Left_Hippocampus: removing 1 voxels in segment 0 label Left_Hippocampus: removing 40 voxels in segment 1 label Left_Hippocampus: removing 212 voxels in segment 2 label Left_Hippocampus: removing 561 voxels in segment 3 label Left_Hippocampus: removing 47 voxels in segment 4 label Left_Hippocampus: removing 8 voxels in segment 6 label Right_Hippocampus: removing 16 voxels in segment 1 label Left_Amygdala: removing 4 voxels in segment 1 label Left_Amygdala: removing 32 voxels in segment 2 label Left_Amygdala: removing 10 voxels in segment 3 label Left_Amygdala: removing 2 voxels in segment 4 label Left_Amygdala: removing 4 voxels in segment 5 generating cortex label... 17 non-cortical segments detected only using segment with 1724 vertices erasing segment 0 (vno[0] = 49161) erasing segment 2 (vno[0] = 78990) erasing segment 3 (vno[0] = 80863) erasing segment 4 (vno[0] = 85370) erasing segment 5 (vno[0] = 93415) erasing segment 6 (vno[0] = 94125) erasing segment 7 (vno[0] = 95190) erasing segment 8 (vno[0] = 95217) erasing segment 9 (vno[0] = 95218) erasing segment 10 (vno[0] = 96359) erasing segment 11 (vno[0] = 102030) erasing segment 12 (vno[0] = 105040) erasing segment 13 (vno[0] = 105051) erasing segment 14 (vno[0] = 106063) erasing segment 15 (vno[0] = 107223) erasing segment 16 (vno[0] = 108279) writing cortex label to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/label/lh.cortex.label... LabelWrite: saving to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/label/lh.cortex.label writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.curv writing smoothed area to lh.area writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.area vertex spacing 0.90 +- 0.27 (0.05-->5.49) (max @ vno 96388 --> 96387) face area 0.34 +- 0.17 (0.00-->4.93) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=58.3, 209 (209) missing vertices, mean dist 1.8 [0.5 (%0.0)->3.0 (%100.0))] %15 local maxima, %41 large gradients and %41 min vals, 4061 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=21272056.0, rms=25.87 001: dt: 0.5000, sse=16054905.0, rms=21.80 002: dt: 0.5000, sse=12457340.0, rms=18.49 003: dt: 0.5000, sse=10102452.0, rms=15.85 004: dt: 0.5000, sse=8724372.0, rms=13.77 005: dt: 0.5000, sse=7937465.5, rms=12.18 006: dt: 0.5000, sse=7466873.5, rms=10.99 007: dt: 0.5000, sse=7212140.5, rms=10.08 008: dt: 0.5000, sse=7080993.5, rms=9.34 009: dt: 0.5000, sse=7074060.0, rms=8.74 010: dt: 0.5000, sse=7146361.5, rms=8.21 011: dt: 0.5000, sse=7254057.0, rms=7.75 012: dt: 0.5000, sse=7371124.0, rms=7.32 013: dt: 0.5000, sse=7474794.0, rms=6.92 014: dt: 0.5000, sse=7655475.5, rms=6.56 015: dt: 0.5000, sse=7720326.0, rms=6.23 016: dt: 0.5000, sse=7931089.5, rms=5.93 017: dt: 0.5000, sse=7980381.5, rms=5.66 018: dt: 0.5000, sse=8115254.0, rms=5.44 019: dt: 0.5000, sse=8163081.0, rms=5.27 020: dt: 0.5000, sse=8268768.0, rms=5.13 021: dt: 0.5000, sse=8283052.0, rms=5.02 022: dt: 0.5000, sse=8357982.5, rms=4.95 023: dt: 0.5000, sse=8370108.0, rms=4.88 024: dt: 0.5000, sse=8436540.0, rms=4.81 rms = 4.77, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=8417335.0, rms=4.77 026: dt: 0.2500, sse=7142369.5, rms=4.54 027: dt: 0.2500, sse=7034317.0, rms=4.47 rms = 4.46, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=6983759.0, rms=4.46 029: dt: 0.1250, sse=6754678.5, rms=4.41 rms = 4.39, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=6729608.0, rms=4.39 positioning took 3.4 minutes mean border=56.8, 2032 (44) missing vertices, mean dist 0.3 [0.3 (%44.3)->1.0 (%55.7))] %32 local maxima, %29 large gradients and %33 min vals, 2113 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7355019.0, rms=5.46 031: dt: 0.5000, sse=7584129.0, rms=5.12 032: dt: 0.5000, sse=8864351.0, rms=4.91 rms = 4.86, time step reduction 1 of 3 to 0.250... 033: dt: 0.5000, sse=8651753.0, rms=4.86 034: dt: 0.2500, sse=7868875.5, rms=4.55 035: dt: 0.2500, sse=7855056.0, rms=4.44 rms = 4.42, time step reduction 2 of 3 to 0.125... 036: dt: 0.2500, sse=7852655.5, rms=4.42 037: dt: 0.1250, sse=7649642.0, rms=4.33 rms = 4.30, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=7643159.0, rms=4.30 positioning took 0.9 minutes mean border=56.1, 2470 (26) missing vertices, mean dist 0.2 [0.3 (%42.0)->0.7 (%58.0))] %43 local maxima, %17 large gradients and %34 min vals, 2215 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7736473.5, rms=4.52 rms = 4.58, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=7606671.0, rms=4.38 040: dt: 0.2500, sse=7651295.5, rms=4.29 rms = 4.27, time step reduction 2 of 3 to 0.125... 041: dt: 0.2500, sse=7876718.0, rms=4.27 042: dt: 0.1250, sse=7750235.0, rms=4.16 rms = 4.13, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=7823411.0, rms=4.13 positioning took 0.6 minutes mean border=55.7, 5373 (21) missing vertices, mean dist 0.1 [0.3 (%43.8)->0.5 (%56.2))] %46 local maxima, %14 large gradients and %33 min vals, 2242 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=7830389.0, rms=4.15 rms = 4.20, time step reduction 1 of 3 to 0.250... 044: dt: 0.2500, sse=7818709.0, rms=4.05 045: dt: 0.2500, sse=8203385.0, rms=3.95 rms = 3.92, time step reduction 2 of 3 to 0.125... 046: dt: 0.2500, sse=8395024.0, rms=3.92 047: dt: 0.1250, sse=8307165.0, rms=3.81 rms = 3.77, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=8365787.5, rms=3.77 positioning took 0.6 minutes writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.area.pial vertex spacing 1.07 +- 0.50 (0.05-->9.40) (max @ vno 95258 --> 95250) face area 0.45 +- 0.39 (0.00-->9.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 140905 vertices processed 25000 of 140905 vertices processed 50000 of 140905 vertices processed 75000 of 140905 vertices processed 100000 of 140905 vertices processed 125000 of 140905 vertices processed 0 of 140905 vertices processed 25000 of 140905 vertices processed 50000 of 140905 vertices processed 75000 of 140905 vertices processed 100000 of 140905 vertices processed 125000 of 140905 vertices processed thickness calculation complete, 4814:5027 truncations. 40754 vertices at 0 distance 63580 vertices at 1 distance 74096 vertices at 2 distance 49805 vertices at 3 distance 23895 vertices at 4 distance 9895 vertices at 5 distance 4222 vertices at 6 distance 1962 vertices at 7 distance 1001 vertices at 8 distance 582 vertices at 9 distance 373 vertices at 10 distance 253 vertices at 11 distance 217 vertices at 12 distance 156 vertices at 13 distance 106 vertices at 14 distance 82 vertices at 15 distance 74 vertices at 16 distance 58 vertices at 17 distance 66 vertices at 18 distance 53 vertices at 19 distance 112 vertices at 20 distance writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.thickness positioning took 15.0 minutes #-------------------------------------------- #@# Surf Volume lh Mon Apr 30 20:20:44 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness #-------------------------------------------- #@# Smooth2 lh Mon Apr 30 20:20:45 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Mon Apr 30 20:20:50 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 47.7 mm, total surface area = 86401 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.070 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.050 (target=0.015) step 025: RMS=0.044 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.025 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. inflation took 1.0 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 338 vertices thresholded to be in k1 ~ [-0.36 0.39], k2 ~ [-0.14 0.10] total integrated curvature = 0.318*4pi (3.999) --> 1 handles ICI = 1.4, FI = 11.1, variation=182.004 201 vertices thresholded to be in [-0.03 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 167 vertices thresholded to be in [-0.19 0.14] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.018, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Mon Apr 30 20:23:22 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm NF108_11 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 [ NF108_11/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 273 ] WARN: S lookup min: -1.518872 WARN: S explicit min: 0.000000 vertex = 207 #-------------------------------------------- #@# Sphere lh Mon Apr 30 20:23:27 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/lh.sphere spherical transformation took 1.67 hours scaling brain by 0.272... pass 1: epoch 1 of 3 starting distance error %22.21 pass 1: epoch 2 of 3 starting distance error %22.16 unfolding complete - removing small folds... starting distance error %21.78 removing remaining folds... final distance error %21.80 420: 0 negative triangles #-------------------------------------------- #@# Surf Reg lh Mon Apr 30 22:03:35 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_register -curv ../surf/lh.sphere /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing registered surface to ../surf/lh.sphere.reg... curvature mean = 0.000, std = 0.603 curvature mean = 0.008, std = 0.935 curvature mean = 0.023, std = 0.859 curvature mean = -0.019, std = 0.953 curvature mean = 0.010, std = 0.938 curvature mean = -0.020, std = 0.966 curvature mean = 0.004, std = 0.971 curvature mean = -0.024, std = 0.967 curvature mean = 0.001, std = 0.987 curvature mean = -0.044, std = 0.371 curvature mean = 0.000, std = 0.067 curvature mean = 0.081, std = 0.270 curvature mean = -0.000, std = 0.080 curvature mean = 0.060, std = 0.414 curvature mean = -0.000, std = 0.087 curvature mean = 0.037, std = 0.542 curvature mean = -0.000, std = 0.090 curvature mean = 0.013, std = 0.666 expanding nbhd size to 1 1157: 77 negative triangles #-------------------------------------------- #@# Jacobian white lh Mon Apr 30 23:14:50 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 Mon Apr 30 23:14:53 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mrisp_paint -a 5 /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /export/data1/tools/freesurfer/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Mon Apr 30 23:14:55 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 lh ../surf/lh.sphere.reg /export/data1/tools/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1258 labels changed using aseg relabeling using gibbs priors... 000: 3266 changed, 140905 examined... 001: 746 changed, 14030 examined... 002: 169 changed, 4050 examined... 003: 67 changed, 1049 examined... 004: 24 changed, 377 examined... 005: 8 changed, 159 examined... 006: 4 changed, 47 examined... 007: 7 changed, 28 examined... 008: 2 changed, 32 examined... 009: 1 changed, 13 examined... 010: 0 changed, 7 examined... 261 labels changed using aseg 000: 133 total segments, 92 labels (403 vertices) changed 001: 42 total segments, 1 labels (1 vertices) changed 002: 41 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 36 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1692 vertices marked for relabeling... 1692 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 52 seconds. #----------------------------------------- #@# Parcellation Stats lh Mon Apr 30 23:15:47 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/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 NF108_11 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/wm.mgz... reading input surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.white... reading input pial surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.pial... reading input white surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/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 1694 1180 3341 2.709 0.602 0.114 0.033 15 2.1 bankssts 1155 771 2329 2.702 0.831 0.153 0.063 27 2.9 caudalanteriorcingulate 3610 2460 7894 2.792 0.727 0.144 0.064 69 9.1 caudalmiddlefrontal 2114 1492 4612 2.678 0.676 0.189 0.121 76 7.2 cuneus 703 472 2241 3.400 0.964 0.190 0.411 35 17.0 entorhinal 5908 4136 15079 3.038 0.695 0.157 0.075 133 17.8 fusiform 8111 5531 23473 3.281 0.940 0.170 0.104 228 37.4 inferiorparietal 6767 4655 16871 2.966 0.862 0.161 0.089 241 23.4 inferiortemporal 1531 1018 3719 3.105 0.921 0.166 0.066 32 4.0 isthmuscingulate 7904 5503 17272 2.607 0.785 0.175 0.104 214 27.9 lateraloccipital 3878 2581 9115 2.777 0.871 0.169 0.229 472 17.3 lateralorbitofrontal 4098 2826 8523 2.701 0.727 0.188 0.126 184 20.6 lingual 2630 1747 6227 2.963 0.990 0.157 0.131 227 17.2 medialorbitofrontal 5387 3603 14410 2.991 0.839 0.155 0.074 121 16.8 middletemporal 1226 792 3002 3.109 0.774 0.122 0.071 18 2.4 parahippocampal 2002 1421 4640 2.695 0.780 0.159 0.061 34 5.5 paracentral 2532 1749 6211 2.800 0.737 0.153 0.077 71 7.2 parsopercularis 1316 855 3617 3.045 0.979 0.207 0.165 51 8.1 parsorbitalis 1876 1266 4386 2.687 0.984 0.143 0.065 35 4.9 parstriangularis 1683 1140 2912 2.416 0.800 0.158 0.084 31 4.7 pericalcarine 6741 4508 13265 2.504 0.870 0.176 0.215 274 81.0 postcentral 1989 1308 4105 2.735 0.866 0.150 0.057 39 4.4 posteriorcingulate 6856 4539 14917 2.867 0.677 0.141 0.056 102 15.8 precentral 5337 3673 12883 2.876 0.817 0.151 0.070 110 14.3 precuneus 1120 734 2817 3.233 0.928 0.163 0.141 72 6.7 rostralanteriorcingulate 9185 6053 19791 2.669 0.875 0.183 0.141 370 50.3 rostralmiddlefrontal 10157 6926 26318 3.155 0.888 0.149 0.103 225 31.3 superiorfrontal 8111 5585 19018 2.793 0.799 0.156 0.083 177 23.5 superiorparietal 5708 3869 14675 3.154 0.690 0.142 0.068 114 15.8 superiortemporal 6678 4529 17010 2.963 0.852 0.163 0.088 178 23.2 supramarginal 362 253 981 2.576 0.990 0.211 0.109 10 1.7 frontalpole 875 624 2853 3.046 1.062 0.173 0.101 20 3.6 temporalpole 782 490 1599 3.138 0.483 0.145 0.049 11 1.6 transversetemporal 3618 2314 8569 3.470 0.998 0.124 0.092 112 12.8 insula #----------------------------------------- #@# Cortical Parc 2 lh Mon Apr 30 23:16:04 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 NF108_11 lh ../surf/lh.sphere.reg /export/data1/tools/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading atlas from /export/data1/tools/freesurfer/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 7 labels changed using aseg relabeling using gibbs priors... 000: 9564 changed, 140905 examined... 001: 2434 changed, 36628 examined... 002: 761 changed, 12386 examined... 003: 370 changed, 4253 examined... 004: 173 changed, 2036 examined... 005: 76 changed, 927 examined... 006: 34 changed, 426 examined... 007: 20 changed, 205 examined... 008: 14 changed, 113 examined... 009: 6 changed, 78 examined... 010: 3 changed, 29 examined... 011: 1 changed, 17 examined... 012: 1 changed, 7 examined... 013: 0 changed, 7 examined... 4 labels changed using aseg 000: 312 total segments, 232 labels (2804 vertices) changed 001: 100 total segments, 20 labels (69 vertices) changed 002: 81 total segments, 1 labels (1 vertices) changed 003: 80 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 125 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 901 vertices marked for relabeling... 901 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 59 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Mon Apr 30 23:17:03 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/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 NF108_11 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/wm.mgz... reading input surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.white... reading input pial surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/lh.pial... reading input white surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/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 1323 862 2519 2.618 0.894 0.204 0.141 43 6.7 G_and_S_frontomargin 1557 1097 3845 2.705 0.885 0.195 0.183 73 6.9 G_and_S_occipital_inf 1325 913 3310 2.738 0.706 0.175 0.095 30 4.6 G_and_S_paracentral 1682 1128 4722 3.263 0.672 0.158 0.066 34 4.6 G_and_S_subcentral 931 618 2326 2.873 1.105 0.202 0.512 41 5.5 G_and_S_transv_frontopol 2206 1503 4966 2.882 0.885 0.154 0.109 100 9.2 G_and_S_cingul-Ant 1620 1108 3312 2.625 0.713 0.135 0.049 26 3.3 G_and_S_cingul-Mid-Ant 1749 1167 3626 2.868 0.787 0.139 0.054 28 3.6 G_and_S_cingul-Mid-Post 529 354 1799 3.482 0.827 0.200 0.092 18 2.1 G_cingul-Post-dorsal 336 230 983 3.383 0.698 0.189 0.098 9 1.3 G_cingul-Post-ventral 1789 1263 4412 2.795 0.741 0.208 0.154 62 7.5 G_cuneus 1650 1118 4797 3.149 0.661 0.173 0.102 66 6.2 G_front_inf-Opercular 449 289 1703 3.783 0.625 0.205 0.115 21 1.8 G_front_inf-Orbital 958 632 3232 3.316 0.859 0.181 0.109 26 4.1 G_front_inf-Triangul 4652 3054 12721 2.946 0.833 0.199 0.164 208 29.5 G_front_middle 6592 4483 20208 3.483 0.767 0.168 0.091 191 26.2 G_front_sup 512 306 1585 4.183 1.044 0.130 0.147 31 3.6 G_Ins_lg_and_S_cent_ins 724 442 2596 3.976 0.605 0.157 0.119 40 2.6 G_insular_short 2971 2043 9157 3.136 1.019 0.197 0.113 88 13.2 G_occipital_middle 1754 1212 3961 2.744 0.742 0.186 0.133 65 6.8 G_occipital_sup 2435 1655 7225 3.251 0.637 0.173 0.084 68 8.9 G_oc-temp_lat-fusifor 2667 1869 6431 2.725 0.773 0.210 0.129 99 14.4 G_oc-temp_med-Lingual 1608 1079 5230 3.512 0.891 0.156 0.223 47 18.6 G_oc-temp_med-Parahip 2743 1749 7399 2.985 0.946 0.209 0.188 346 21.0 G_orbital 3077 2116 11877 3.669 0.907 0.180 0.101 91 12.8 G_pariet_inf-Angular 3688 2505 10942 3.156 0.854 0.186 0.117 137 17.2 G_pariet_inf-Supramar 3553 2496 10392 2.957 0.824 0.171 0.093 88 12.0 G_parietal_sup 2583 1659 5191 2.497 0.900 0.223 0.385 170 60.5 G_postcentral 2325 1528 6511 3.110 0.561 0.163 0.075 50 7.3 G_precentral 2560 1795 8277 3.257 0.866 0.192 0.109 85 10.4 G_precuneus 910 610 2535 2.901 0.883 0.179 0.204 176 11.1 G_rectus 586 364 1167 3.372 0.896 0.142 0.153 28 4.0 G_subcallosal 583 356 1400 3.139 0.436 0.143 0.052 9 1.3 G_temp_sup-G_T_transv 2213 1469 7039 3.278 0.738 0.172 0.117 78 10.3 G_temp_sup-Lateral 718 501 2107 3.654 0.781 0.134 0.075 17 1.4 G_temp_sup-Plan_polar 1059 731 2520 2.764 0.748 0.134 0.042 14 2.0 G_temp_sup-Plan_tempo 4215 2881 11907 3.046 0.932 0.183 0.120 223 20.1 G_temporal_inf 3505 2328 11059 3.130 0.901 0.175 0.108 112 16.4 G_temporal_middle 300 204 441 2.058 0.582 0.112 0.025 2 0.3 Lat_Fis-ant-Horizont 306 210 687 2.752 0.790 0.122 0.033 3 0.4 Lat_Fis-ant-Vertical 1340 890 2099 2.649 0.624 0.125 0.046 11 2.3 Lat_Fis-post 2471 1719 5042 2.421 0.650 0.172 0.086 62 8.1 Pole_occipital 2132 1514 6631 2.955 0.953 0.183 0.104 59 9.0 Pole_temporal 2156 1451 3749 2.606 0.756 0.154 0.095 52 6.6 S_calcarine 3051 2056 4301 2.282 0.554 0.131 0.117 68 16.8 S_central 1144 828 2133 2.393 0.630 0.130 0.038 13 2.0 S_cingul-Marginalis 588 392 1039 2.775 0.617 0.101 0.023 3 0.6 S_circular_insula_ant 1476 1009 3031 3.470 0.750 0.092 0.022 7 1.3 S_circular_insula_inf 2004 1373 3312 2.546 0.727 0.108 0.034 14 3.0 S_circular_insula_sup 1496 1047 3037 3.099 0.565 0.123 0.064 21 2.6 S_collat_transv_ant 457 303 626 2.120 0.416 0.138 0.055 8 1.3 S_collat_transv_post 3274 2213 5215 2.252 0.693 0.128 0.049 39 6.8 S_front_inf 1285 878 2792 2.960 0.800 0.172 0.140 70 7.6 S_front_middle 2766 1949 4871 2.405 0.700 0.120 0.039 23 4.6 S_front_sup 426 274 716 2.781 0.935 0.144 0.052 5 1.1 S_interm_prim-Jensen 2489 1703 4626 2.872 0.708 0.132 0.050 33 4.6 S_intrapariet_and_P_trans 719 488 1398 2.759 0.846 0.158 0.080 12 1.9 S_oc_middle_and_Lunatus 1260 854 1990 2.642 0.634 0.145 0.069 22 3.8 S_oc_sup_and_transversal 1073 747 1658 2.423 0.523 0.125 0.039 9 1.8 S_occipital_ant 1044 742 1975 2.768 0.614 0.129 0.043 11 1.8 S_oc-temp_lat 2254 1560 3841 2.726 0.542 0.128 0.055 72 5.6 S_oc-temp_med_and_Lingual 537 345 1149 3.267 0.749 0.150 0.063 9 1.3 S_orbital_lateral 582 402 1153 2.589 1.128 0.136 0.856 172 1.5 S_orbital_med-olfact 1478 1010 2829 2.454 0.795 0.162 0.078 29 4.4 S_orbital-H_Shaped 2149 1433 3508 2.563 0.596 0.119 0.045 40 3.6 S_parieto_occipital 1478 904 2157 2.590 0.989 0.147 0.044 29 2.6 S_pericallosal 3359 2304 5351 2.313 0.754 0.130 0.040 35 5.8 S_postcentral 1661 1117 2783 2.612 0.561 0.123 0.040 17 2.6 S_precentral-inf-part 883 605 1469 2.742 0.698 0.114 0.031 6 1.2 S_precentral-sup-part 587 397 1300 3.057 0.914 0.147 0.066 10 1.5 S_suborbital 993 666 1771 2.616 0.655 0.122 0.041 10 1.8 S_subparietal 1871 1252 2798 2.600 0.578 0.124 0.041 17 3.0 S_temporal_inf 5689 3904 11199 2.865 0.697 0.134 0.060 94 16.4 S_temporal_sup 529 349 1007 2.954 0.674 0.105 0.029 4 0.5 S_temporal_transverse #-------------------------------------------- #@# Tessellate rh Mon Apr 30 23:17:22 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 4 found - 4 modified | TOTAL: 5 pass 2 (yz+): 0 found - 4 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 3 found - 3 modified | TOTAL: 9 pass 2 (xz+): 0 found - 3 modified | TOTAL: 9 pass 1 (xz-): 3 found - 3 modified | TOTAL: 12 pass 2 (xz-): 0 found - 3 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 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 Iteration Number : 1 pass 1 (++): 3 found - 3 modified | TOTAL: 3 pass 2 (++): 0 found - 3 modified | TOTAL: 3 pass 1 (+-): 1 found - 1 modified | TOTAL: 4 pass 2 (+-): 0 found - 1 modified | TOTAL: 4 pass 1 (--): 2 found - 2 modified | TOTAL: 6 pass 2 (--): 0 found - 2 modified | TOTAL: 6 pass 1 (-+): 0 found - 0 modified | TOTAL: 6 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 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 Iteration Number : 3 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 : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 22 (out of 239940: 0.009169) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ slice 30: 131 vertices, 161 faces slice 40: 3961 vertices, 4202 faces slice 50: 12025 vertices, 12377 faces slice 60: 22169 vertices, 22558 faces slice 70: 33702 vertices, 34169 faces slice 80: 45479 vertices, 45896 faces slice 90: 57194 vertices, 57667 faces slice 100: 69390 vertices, 69881 faces slice 110: 80705 vertices, 81186 faces slice 120: 91392 vertices, 91870 faces slice 130: 101827 vertices, 102316 faces slice 140: 111685 vertices, 112090 faces slice 150: 119899 vertices, 120295 faces slice 160: 127064 vertices, 127432 faces slice 170: 133380 vertices, 133713 faces slice 180: 138121 vertices, 138411 faces slice 190: 141376 vertices, 141611 faces slice 200: 142154 vertices, 142298 faces slice 210: 142154 vertices, 142298 faces slice 220: 142154 vertices, 142298 faces slice 230: 142154 vertices, 142298 faces slice 240: 142154 vertices, 142298 faces slice 250: 142154 vertices, 142298 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... 142154 voxel in cpt #1: X=-144 [v=142154,e=426894,f=284596] located at (24.185616, -24.720205, 29.267822) For the whole surface: X=-144 [v=142154,e=426894,f=284596] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Mon Apr 30 23:17:32 EDT 2012 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Mon Apr 30 23:17:37 EDT 2012 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts avg radius = 47.3 mm, total surface area = 73975 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.1 minutes Not saving sulc step 000: RMS=0.113 (target=0.015) step 005: RMS=0.087 (target=0.015) step 010: RMS=0.069 (target=0.015) step 015: RMS=0.062 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.051 (target=0.015) step 030: RMS=0.047 (target=0.015) step 035: RMS=0.045 (target=0.015) step 040: RMS=0.044 (target=0.015) step 045: RMS=0.042 (target=0.015) step 050: RMS=0.040 (target=0.015) step 055: RMS=0.039 (target=0.015) step 060: RMS=0.039 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Mon Apr 30 23:18:41 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/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 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.96 +- 0.60 (0.00-->6.97) (max @ vno 102644 --> 103775) face area 0.02 +- 0.03 (-0.14-->0.69) scaling brain by 0.301... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.090, avgs=0 005/300: dt: 0.9000, rms radial error=176.834, avgs=0 010/300: dt: 0.9000, rms radial error=176.283, avgs=0 015/300: dt: 0.9000, rms radial error=175.553, avgs=0 020/300: dt: 0.9000, rms radial error=174.720, avgs=0 025/300: dt: 0.9000, rms radial error=173.829, avgs=0 030/300: dt: 0.9000, rms radial error=172.907, avgs=0 035/300: dt: 0.9000, rms radial error=171.970, avgs=0 040/300: dt: 0.9000, rms radial error=171.026, avgs=0 045/300: dt: 0.9000, rms radial error=170.079, avgs=0 050/300: dt: 0.9000, rms radial error=169.133, avgs=0 055/300: dt: 0.9000, rms radial error=168.189, avgs=0 060/300: dt: 0.9000, rms radial error=167.249, avgs=0 065/300: dt: 0.9000, rms radial error=166.313, avgs=0 070/300: dt: 0.9000, rms radial error=165.381, avgs=0 075/300: dt: 0.9000, rms radial error=164.454, avgs=0 080/300: dt: 0.9000, rms radial error=163.532, avgs=0 085/300: dt: 0.9000, rms radial error=162.615, avgs=0 090/300: dt: 0.9000, rms radial error=161.702, avgs=0 095/300: dt: 0.9000, rms radial error=160.795, avgs=0 100/300: dt: 0.9000, rms radial error=159.893, avgs=0 105/300: dt: 0.9000, rms radial error=158.995, avgs=0 110/300: dt: 0.9000, rms radial error=158.102, avgs=0 115/300: dt: 0.9000, rms radial error=157.214, avgs=0 120/300: dt: 0.9000, rms radial error=156.330, avgs=0 125/300: dt: 0.9000, rms radial error=155.451, avgs=0 130/300: dt: 0.9000, rms radial error=154.577, avgs=0 135/300: dt: 0.9000, rms radial error=153.708, avgs=0 140/300: dt: 0.9000, rms radial error=152.843, avgs=0 145/300: dt: 0.9000, rms radial error=151.982, avgs=0 150/300: dt: 0.9000, rms radial error=151.127, avgs=0 155/300: dt: 0.9000, rms radial error=150.276, avgs=0 160/300: dt: 0.9000, rms radial error=149.429, avgs=0 165/300: dt: 0.9000, rms radial error=148.587, avgs=0 170/300: dt: 0.9000, rms radial error=147.750, avgs=0 175/300: dt: 0.9000, rms radial error=146.917, avgs=0 180/300: dt: 0.9000, rms radial error=146.089, avgs=0 185/300: dt: 0.9000, rms radial error=145.265, avgs=0 190/300: dt: 0.9000, rms radial error=144.446, avgs=0 195/300: dt: 0.9000, rms radial error=143.631, avgs=0 200/300: dt: 0.9000, rms radial error=142.821, avgs=0 205/300: dt: 0.9000, rms radial error=142.016, avgs=0 210/300: dt: 0.9000, rms radial error=141.215, avgs=0 215/300: dt: 0.9000, rms radial error=140.418, avgs=0 220/300: dt: 0.9000, rms radial error=139.626, avgs=0 225/300: dt: 0.9000, rms radial error=138.838, avgs=0 230/300: dt: 0.9000, rms radial error=138.055, avgs=0 235/300: dt: 0.9000, rms radial error=137.275, avgs=0 240/300: dt: 0.9000, rms radial error=136.500, avgs=0 245/300: dt: 0.9000, rms radial error=135.729, avgs=0 250/300: dt: 0.9000, rms radial error=134.963, avgs=0 255/300: dt: 0.9000, rms radial error=134.201, avgs=0 260/300: dt: 0.9000, rms radial error=133.443, avgs=0 265/300: dt: 0.9000, rms radial error=132.689, avgs=0 270/300: dt: 0.9000, rms radial error=131.939, avgs=0 275/300: dt: 0.9000, rms radial error=131.194, avgs=0 280/300: dt: 0.9000, rms radial error=130.453, avgs=0 285/300: dt: 0.9000, rms radial error=129.716, avgs=0 290/300: dt: 0.9000, rms radial error=128.983, avgs=0 295/300: dt: 0.9000, rms radial error=128.254, avgs=0 300/300: dt: 0.9000, rms radial error=127.529, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 7364.86 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 2 (K=80.0), pass 1, starting sse = 1053.07 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 3 (K=320.0), pass 1, starting sse = 103.31 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00385 epoch 4 (K=1280.0), pass 1, starting sse = 11.72 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00752 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.10 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Mon Apr 30 23:24:45 EDT 2012 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 NF108_11 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 1.44 2010/05/27 23:37:16 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ before topology correction, eno=-144 (nv=142154, nf=284596, ne=426894, g=73) 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... 9479 ambiguous faces found in tessellation segmenting defects... 84 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 37 into 36 -merging segment 57 into 52 -merging segment 61 into 63 81 defects to be corrected 0 vertices coincident reading input surface /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4694 (-4.7347) -vertex loglikelihood: -6.4316 (-3.2158) -normal dot loglikelihood: -3.6292 (-3.6292) -quad curv loglikelihood: -6.2664 (-3.1332) Total Loglikelihood : -25.7967 CORRECTING DEFECT 0 (vertices=5, convex hull=13) After retessellation of defect 0, euler #=-77 (136176,405688,269435) : difference with theory (-78) = -1 CORRECTING DEFECT 1 (vertices=15, convex hull=24) After retessellation of defect 1, euler #=-76 (136177,405701,269448) : difference with theory (-77) = -1 CORRECTING DEFECT 2 (vertices=11, convex hull=17) After retessellation of defect 2, euler #=-75 (136177,405709,269457) : difference with theory (-76) = -1 CORRECTING DEFECT 3 (vertices=195, convex hull=158) After retessellation of defect 3, euler #=-74 (136228,405932,269630) : difference with theory (-75) = -1 CORRECTING DEFECT 4 (vertices=108, convex hull=126) After retessellation of defect 4, euler #=-73 (136277,406140,269790) : difference with theory (-74) = -1 CORRECTING DEFECT 5 (vertices=19, convex hull=20) After retessellation of defect 5, euler #=-72 (136278,406151,269801) : difference with theory (-73) = -1 CORRECTING DEFECT 6 (vertices=154, convex hull=175) After retessellation of defect 6, euler #=-72 (136322,406379,269985) : difference with theory (-72) = 0 CORRECTING DEFECT 7 (vertices=64, convex hull=48) After retessellation of defect 7, euler #=-72 (136331,406430,270027) : difference with theory (-71) = 1 CORRECTING DEFECT 8 (vertices=37, convex hull=48) After retessellation of defect 8, euler #=-71 (136335,406462,270056) : difference with theory (-70) = 1 CORRECTING DEFECT 9 (vertices=29, convex hull=55) After retessellation of defect 9, euler #=-70 (136344,406510,270096) : difference with theory (-69) = 1 CORRECTING DEFECT 10 (vertices=164, convex hull=151) After retessellation of defect 10, euler #=-69 (136394,406736,270273) : difference with theory (-68) = 1 CORRECTING DEFECT 11 (vertices=89, convex hull=81) After retessellation of defect 11, euler #=-68 (136419,406848,270361) : difference with theory (-67) = 1 CORRECTING DEFECT 12 (vertices=12, convex hull=16) After retessellation of defect 12, euler #=-67 (136419,406855,270369) : difference with theory (-66) = 1 CORRECTING DEFECT 13 (vertices=172, convex hull=148) After retessellation of defect 13, euler #=-66 (136446,407006,270494) : difference with theory (-65) = 1 CORRECTING DEFECT 14 (vertices=42, convex hull=74) After retessellation of defect 14, euler #=-65 (136464,407089,270560) : difference with theory (-64) = 1 CORRECTING DEFECT 15 (vertices=53, convex hull=97) After retessellation of defect 15, euler #=-64 (136477,407177,270636) : difference with theory (-63) = 1 CORRECTING DEFECT 16 (vertices=123, convex hull=146) After retessellation of defect 16, euler #=-63 (136519,407367,270785) : difference with theory (-62) = 1 CORRECTING DEFECT 17 (vertices=66, convex hull=104) After retessellation of defect 17, euler #=-62 (136556,407526,270908) : difference with theory (-61) = 1 CORRECTING DEFECT 18 (vertices=92, convex hull=102) After retessellation of defect 18, euler #=-61 (136571,407617,270985) : difference with theory (-60) = 1 CORRECTING DEFECT 19 (vertices=131, convex hull=112) After retessellation of defect 19, euler #=-60 (136610,407789,271119) : difference with theory (-59) = 1 CORRECTING DEFECT 20 (vertices=40, convex hull=20) After retessellation of defect 20, euler #=-59 (136612,407802,271131) : difference with theory (-58) = 1 CORRECTING DEFECT 21 (vertices=61, convex hull=87) After retessellation of defect 21, euler #=-58 (136628,407887,271201) : difference with theory (-57) = 1 CORRECTING DEFECT 22 (vertices=51, convex hull=89) After retessellation of defect 22, euler #=-57 (136637,407956,271262) : difference with theory (-56) = 1 CORRECTING DEFECT 23 (vertices=101, convex hull=99) After retessellation of defect 23, euler #=-56 (136675,408118,271387) : difference with theory (-55) = 1 CORRECTING DEFECT 24 (vertices=17, convex hull=27) After retessellation of defect 24, euler #=-55 (136678,408137,271404) : difference with theory (-54) = 1 CORRECTING DEFECT 25 (vertices=55, convex hull=53) After retessellation of defect 25, euler #=-54 (136688,408188,271446) : difference with theory (-53) = 1 CORRECTING DEFECT 26 (vertices=44, convex hull=83) After retessellation of defect 26, euler #=-53 (136713,408299,271533) : difference with theory (-52) = 1 CORRECTING DEFECT 27 (vertices=29, convex hull=32) After retessellation of defect 27, euler #=-52 (136716,408323,271555) : difference with theory (-51) = 1 CORRECTING DEFECT 28 (vertices=77, convex hull=81) After retessellation of defect 28, euler #=-51 (136747,408449,271651) : difference with theory (-50) = 1 CORRECTING DEFECT 29 (vertices=42, convex hull=99) After retessellation of defect 29, euler #=-50 (136773,408569,271746) : difference with theory (-49) = 1 CORRECTING DEFECT 30 (vertices=35, convex hull=25) After retessellation of defect 30, euler #=-49 (136776,408587,271762) : difference with theory (-48) = 1 CORRECTING DEFECT 31 (vertices=16, convex hull=41) After retessellation of defect 31, euler #=-48 (136784,408627,271795) : difference with theory (-47) = 1 CORRECTING DEFECT 32 (vertices=64, convex hull=70) After retessellation of defect 32, euler #=-47 (136806,408720,271867) : difference with theory (-46) = 1 CORRECTING DEFECT 33 (vertices=31, convex hull=71) After retessellation of defect 33, euler #=-46 (136815,408773,271912) : difference with theory (-45) = 1 CORRECTING DEFECT 34 (vertices=190, convex hull=150) After retessellation of defect 34, euler #=-45 (136880,409039,272114) : difference with theory (-44) = 1 CORRECTING DEFECT 35 (vertices=68, convex hull=84) After retessellation of defect 35, euler #=-44 (136913,409170,272213) : difference with theory (-43) = 1 CORRECTING DEFECT 36 (vertices=87, convex hull=124) After retessellation of defect 36, euler #=-42 (136969,409400,272389) : difference with theory (-42) = 0 CORRECTING DEFECT 37 (vertices=70, convex hull=83) After retessellation of defect 37, euler #=-41 (136988,409493,272464) : difference with theory (-41) = 0 CORRECTING DEFECT 38 (vertices=23, convex hull=66) After retessellation of defect 38, euler #=-40 (136999,409551,272512) : difference with theory (-40) = 0 CORRECTING DEFECT 39 (vertices=108, convex hull=100) After retessellation of defect 39, euler #=-39 (137026,409677,272612) : difference with theory (-39) = 0 CORRECTING DEFECT 40 (vertices=59, convex hull=102) After retessellation of defect 40, euler #=-38 (137048,409785,272699) : difference with theory (-38) = 0 CORRECTING DEFECT 41 (vertices=27, convex hull=64) After retessellation of defect 41, euler #=-37 (137064,409856,272755) : difference with theory (-37) = 0 CORRECTING DEFECT 42 (vertices=425, convex hull=233) After retessellation of defect 42, euler #=-36 (137167,410294,273091) : difference with theory (-36) = 0 CORRECTING DEFECT 43 (vertices=32, convex hull=87) After retessellation of defect 43, euler #=-35 (137188,410398,273175) : difference with theory (-35) = 0 CORRECTING DEFECT 44 (vertices=38, convex hull=85) After retessellation of defect 44, euler #=-34 (137204,410480,273242) : difference with theory (-34) = 0 CORRECTING DEFECT 45 (vertices=18, convex hull=30) After retessellation of defect 45, euler #=-33 (137207,410500,273260) : difference with theory (-33) = 0 CORRECTING DEFECT 46 (vertices=23, convex hull=22) After retessellation of defect 46, euler #=-32 (137208,410510,273270) : difference with theory (-32) = 0 CORRECTING DEFECT 47 (vertices=19, convex hull=15) After retessellation of defect 47, euler #=-31 (137212,410526,273283) : difference with theory (-31) = 0 CORRECTING DEFECT 48 (vertices=50, convex hull=61) After retessellation of defect 48, euler #=-30 (137230,410603,273343) : difference with theory (-30) = 0 CORRECTING DEFECT 49 (vertices=68, convex hull=75) After retessellation of defect 49, euler #=-29 (137267,410746,273450) : difference with theory (-29) = 0 CORRECTING DEFECT 50 (vertices=65, convex hull=44) After retessellation of defect 50, euler #=-28 (137276,410787,273483) : difference with theory (-28) = 0 CORRECTING DEFECT 51 (vertices=192, convex hull=148) After retessellation of defect 51, euler #=-26 (137331,411017,273660) : difference with theory (-27) = -1 CORRECTING DEFECT 52 (vertices=25, convex hull=53) After retessellation of defect 52, euler #=-25 (137343,411072,273704) : difference with theory (-26) = -1 CORRECTING DEFECT 53 (vertices=62, convex hull=85) After retessellation of defect 53, euler #=-24 (137360,411157,273773) : difference with theory (-25) = -1 CORRECTING DEFECT 54 (vertices=6, convex hull=24) After retessellation of defect 54, euler #=-23 (137361,411168,273784) : difference with theory (-24) = -1 CORRECTING DEFECT 55 (vertices=34, convex hull=81) After retessellation of defect 55, euler #=-22 (137376,411247,273849) : difference with theory (-23) = -1 CORRECTING DEFECT 56 (vertices=893, convex hull=406) After retessellation of defect 56, euler #=-22 (137513,411865,274330) : difference with theory (-22) = 0 CORRECTING DEFECT 57 (vertices=80, convex hull=115) After retessellation of defect 57, euler #=-21 (137565,412075,274489) : difference with theory (-21) = 0 CORRECTING DEFECT 58 (vertices=25, convex hull=31) After retessellation of defect 58, euler #=-20 (137569,412097,274508) : difference with theory (-20) = 0 CORRECTING DEFECT 59 (vertices=37, convex hull=85) After retessellation of defect 59, euler #=-19 (137590,412196,274587) : difference with theory (-19) = 0 CORRECTING DEFECT 60 (vertices=73, convex hull=67) After retessellation of defect 60, euler #=-17 (137606,412275,274652) : difference with theory (-18) = -1 CORRECTING DEFECT 61 (vertices=49, convex hull=45) After retessellation of defect 61, euler #=-16 (137613,412315,274686) : difference with theory (-17) = -1 CORRECTING DEFECT 62 (vertices=65, convex hull=40) After retessellation of defect 62, euler #=-15 (137625,412370,274730) : difference with theory (-16) = -1 CORRECTING DEFECT 63 (vertices=40, convex hull=75) After retessellation of defect 63, euler #=-14 (137647,412465,274804) : difference with theory (-15) = -1 CORRECTING DEFECT 64 (vertices=13, convex hull=20) After retessellation of defect 64, euler #=-13 (137651,412485,274821) : difference with theory (-14) = -1 CORRECTING DEFECT 65 (vertices=41, convex hull=84) After retessellation of defect 65, euler #=-12 (137678,412597,274907) : difference with theory (-13) = -1 CORRECTING DEFECT 66 (vertices=25, convex hull=49) After retessellation of defect 66, euler #=-11 (137687,412642,274944) : difference with theory (-12) = -1 CORRECTING DEFECT 67 (vertices=72, convex hull=93) After retessellation of defect 67, euler #=-10 (137714,412762,275038) : difference with theory (-11) = -1 CORRECTING DEFECT 68 (vertices=80, convex hull=100) After retessellation of defect 68, euler #=-9 (137744,412896,275143) : difference with theory (-10) = -1 CORRECTING DEFECT 69 (vertices=60, convex hull=59) After retessellation of defect 69, euler #=-8 (137764,412984,275212) : difference with theory (-9) = -1 CORRECTING DEFECT 70 (vertices=32, convex hull=60) After retessellation of defect 70, euler #=-7 (137780,413055,275268) : difference with theory (-8) = -1 CORRECTING DEFECT 71 (vertices=107, convex hull=91) After retessellation of defect 71, euler #=-6 (137814,413199,275379) : difference with theory (-7) = -1 CORRECTING DEFECT 72 (vertices=49, convex hull=86) After retessellation of defect 72, euler #=-5 (137835,413300,275460) : difference with theory (-6) = -1 CORRECTING DEFECT 73 (vertices=115, convex hull=134) After retessellation of defect 73, euler #=-5 (137867,413462,275590) : difference with theory (-5) = 0 CORRECTING DEFECT 74 (vertices=6, convex hull=15) After retessellation of defect 74, euler #=-4 (137867,413464,275593) : difference with theory (-4) = 0 CORRECTING DEFECT 75 (vertices=15, convex hull=14) After retessellation of defect 75, euler #=-3 (137868,413473,275602) : difference with theory (-3) = 0 CORRECTING DEFECT 76 (vertices=53, convex hull=94) After retessellation of defect 76, euler #=-2 (137898,413605,275705) : difference with theory (-2) = 0 CORRECTING DEFECT 77 (vertices=37, convex hull=75) After retessellation of defect 77, euler #=-1 (137919,413699,275779) : difference with theory (-1) = 0 CORRECTING DEFECT 78 (vertices=26, convex hull=32) After retessellation of defect 78, euler #=0 (137924,413725,275801) : difference with theory (0) = 0 CORRECTING DEFECT 79 (vertices=6, convex hull=25) After retessellation of defect 79, euler #=1 (137924,413731,275808) : difference with theory (1) = 0 CORRECTING DEFECT 80 (vertices=40, convex hull=92) After retessellation of defect 80, euler #=2 (137942,413820,275880) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.26 (0.03-->10.07) (max @ vno 109555 --> 116859) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.26 (0.03-->10.07) (max @ vno 109555 --> 116859) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 223 mutations (32.4%), 466 crossovers (67.6%), 360 vertices were eliminated building final representation... 4212 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=137942, nf=275880, ne=413820, g=0) writing corrected surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 58.6 minutes 0 defective edges removing intersecting faces 000: 656 intersecting 001: 22 intersecting 002: 6 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 137942 - 413820 + 275880 = 2 --> 0 holes F =2V-4: 275880 = 275884-4 (0) 2E=3F: 827640 = 827640 (0) total defect index = 0 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 68 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make Final Surf rh Tue May 1 00:23:28 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs NF108_11 rh 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 1.113 2010/04/08 19:42:02 nicks Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/filled.mgz... reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/brain.finalsurfs.mgz... reading volume /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/mri/wm.mgz... 25122 bright wm thresholded. 33 bright non-wm voxels segmented. reading original surface position from /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.orig... computing class statistics... border white: 252008 voxels (1.50%) border gray 311945 voxels (1.86%) WM (96.0): 96.6 +- 8.9 [70.0 --> 110.0] GM (70.0) : 70.2 +- 9.7 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.3 (was 70) setting MAX_BORDER_WHITE to 110.9 (was 105) setting MIN_BORDER_WHITE to 69.0 (was 85) setting MAX_CSF to 49.5 (was 40) setting MAX_GRAY to 93.1 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 64.1 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 39.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.01-->4.73) (max @ vno 6942 --> 13627) face area 0.28 +- 0.13 (0.00-->3.80) mean absolute distance = 0.63 +- 0.80 3063 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=69 using class modes intead of means.... mean inside = 92.1, mean outside = 74.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=80.2, 259 (259) missing vertices, mean dist 0.2 [0.6 (%40.0)->0.7 (%60.0))] %71 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=local, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.90 +- 0.27 (0.07-->4.89) (max @ vno 6942 --> 13627) face area 0.28 +- 0.14 (0.00-->3.33) mean absolute distance = 0.32 +- 0.54 2799 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5092586.0, rms=9.32 001: dt: 0.5000, sse=6302365.5, rms=6.45 002: dt: 0.5000, sse=7059021.5, rms=5.13 003: dt: 0.5000, sse=7452242.5, rms=4.53 004: dt: 0.5000, sse=7757308.5, rms=4.17 005: dt: 0.5000, sse=7860801.0, rms=4.01 006: dt: 0.5000, sse=7953916.0, rms=3.87 007: dt: 0.5000, sse=7946997.0, rms=3.82 008: dt: 0.5000, sse=8005576.5, rms=3.74 rms = 3.73, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=7955417.0, rms=3.73 010: dt: 0.2500, sse=5272613.0, rms=2.69 011: dt: 0.2500, sse=4871737.0, rms=2.42 012: dt: 0.2500, sse=4659836.5, rms=2.34 013: dt: 0.2500, sse=4591093.0, rms=2.29 rms = 2.25, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4542156.5, rms=2.25 015: dt: 0.1250, sse=4457950.5, rms=2.20 rms = 2.18, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4424230.5, rms=2.18 positioning took 1.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.7, 226 (62) missing vertices, mean dist -0.1 [0.3 (%69.5)->0.3 (%30.5))] %79 local maxima, %16 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.27 (0.09-->5.03) (max @ vno 108755 --> 108772) face area 0.34 +- 0.17 (0.00-->3.93) mean absolute distance = 0.26 +- 0.43 3391 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4814261.0, rms=3.94 017: dt: 0.5000, sse=5480324.5, rms=2.84 rms = 3.23, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5088799.5, rms=2.18 019: dt: 0.2500, sse=4968552.0, rms=1.90 020: dt: 0.2500, sse=4894507.0, rms=1.81 rms = 1.79, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=4845255.5, rms=1.79 rms = 1.75, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=4783056.0, rms=1.75 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 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.2, 216 (38) missing vertices, mean dist -0.1 [0.3 (%61.4)->0.2 (%38.6))] %83 local maxima, %12 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.27 (0.08-->5.17) (max @ vno 108755 --> 108772) face area 0.34 +- 0.17 (0.00-->3.87) mean absolute distance = 0.25 +- 0.39 3619 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4861795.5, rms=2.49 rms = 2.62, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=4831864.5, rms=1.91 024: dt: 0.2500, sse=4907781.5, rms=1.62 rms = 1.59, time step reduction 2 of 3 to 0.125... 025: dt: 0.2500, sse=4992835.0, rms=1.59 rms = 1.55, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=4934128.0, rms=1.55 positioning took 0.5 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 4 vertex label from ripped group mean border=84.9, 229 (33) missing vertices, mean dist -0.0 [0.3 (%52.6)->0.2 (%47.4))] %85 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=4943173.5, rms=1.71 rms = 1.83, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5071366.5, rms=1.35 028: dt: 0.2500, sse=5396268.5, rms=1.19 rms = 1.20, time step reduction 2 of 3 to 0.125... rms = 1.19, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5389492.0, rms=1.19 positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... label Right_Hippocampus: removing 16 voxels in segment 0 label Right_Hippocampus: removing 68 voxels in segment 1 label Right_Hippocampus: removing 1670 voxels in segment 2 label Right_Hippocampus: removing 3 voxels in segment 3 label Right_Hippocampus: removing 6 voxels in segment 4 label Right_Hippocampus: removing 5 voxels in segment 5 label Right_Hippocampus: removing 7234 voxels in segment 6 label Right_Hippocampus: removing 1 voxels in segment 7 label Right_Hippocampus: removing 33 voxels in segment 9 label Right_Hippocampus: removing 182 voxels in segment 10 label Right_Hippocampus: removing 24001 voxels in segment 11 label Right_Amygdala: removing 253 voxels in segment 1 label Right_Amygdala: removing 1 voxels in segment 2 label Right_Amygdala: removing 961 voxels in segment 3 generating cortex label... 22 non-cortical segments detected only using segment with 1746 vertices erasing segment 1 (vno[0] = 64826) erasing segment 2 (vno[0] = 82572) erasing segment 3 (vno[0] = 89594) erasing segment 4 (vno[0] = 93389) erasing segment 5 (vno[0] = 93505) erasing segment 6 (vno[0] = 94455) erasing segment 7 (vno[0] = 94516) erasing segment 8 (vno[0] = 96760) erasing segment 9 (vno[0] = 98579) erasing segment 10 (vno[0] = 100787) erasing segment 11 (vno[0] = 101708) erasing segment 12 (vno[0] = 101720) erasing segment 13 (vno[0] = 102607) erasing segment 14 (vno[0] = 103513) erasing segment 15 (vno[0] = 104474) erasing segment 16 (vno[0] = 106297) erasing segment 17 (vno[0] = 107950) erasing segment 18 (vno[0] = 109513) erasing segment 19 (vno[0] = 111162) erasing segment 20 (vno[0] = 137366) erasing segment 21 (vno[0] = 137438) writing cortex label to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/label/rh.cortex.label... LabelWrite: saving to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/label/rh.cortex.label writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.curv writing smoothed area to rh.area writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.area vertex spacing 0.90 +- 0.27 (0.05-->5.25) (max @ vno 108755 --> 108772) face area 0.34 +- 0.17 (0.00-->3.98) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=60.4, 263 (263) missing vertices, mean dist 1.8 [1.2 (%0.0)->2.8 (%100.0))] %18 local maxima, %44 large gradients and %33 min vals, 3198 gradients ignored tol=1.0e-04, sigma=2.0, host=local, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=18871992.0, rms=24.47 001: dt: 0.5000, sse=14067902.0, rms=20.37 002: dt: 0.5000, sse=10816410.0, rms=17.04 003: dt: 0.5000, sse=8870595.0, rms=14.46 004: dt: 0.5000, sse=7900996.0, rms=12.48 005: dt: 0.5000, sse=7296373.0, rms=10.95 006: dt: 0.5000, sse=6942588.0, rms=9.80 007: dt: 0.5000, sse=6733682.5, rms=8.91 008: dt: 0.5000, sse=6620692.0, rms=8.19 009: dt: 0.5000, sse=6621206.0, rms=7.58 010: dt: 0.5000, sse=6620400.5, rms=7.07 011: dt: 0.5000, sse=6707041.0, rms=6.65 012: dt: 0.5000, sse=6792023.5, rms=6.27 013: dt: 0.5000, sse=6906148.0, rms=5.95 014: dt: 0.5000, sse=7008748.0, rms=5.63 015: dt: 0.5000, sse=7109228.5, rms=5.36 016: dt: 0.5000, sse=7227036.5, rms=5.10 017: dt: 0.5000, sse=7295843.5, rms=4.90 018: dt: 0.5000, sse=7382326.5, rms=4.71 019: dt: 0.5000, sse=7449616.0, rms=4.58 020: dt: 0.5000, sse=7558204.0, rms=4.47 021: dt: 0.5000, sse=7562661.0, rms=4.39 022: dt: 0.5000, sse=7681229.5, rms=4.32 023: dt: 0.5000, sse=7699355.5, rms=4.26 024: dt: 0.5000, sse=7738371.0, rms=4.21 rms = 4.18, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=7721195.5, rms=4.18 026: dt: 0.2500, sse=6547018.5, rms=3.97 027: dt: 0.2500, sse=6445637.0, rms=3.91 rms = 3.90, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=6401119.5, rms=3.90 rms = 3.87, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=6233635.0, rms=3.87 positioning took 3.1 minutes mean border=58.5, 1872 (77) missing vertices, mean dist 0.4 [0.3 (%42.3)->1.2 (%57.7))] %37 local maxima, %30 large gradients and %28 min vals, 1654 gradients ignored tol=1.0e-04, sigma=1.0, host=local, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=6927497.0, rms=5.39 030: dt: 0.5000, sse=7027976.0, rms=4.89 031: dt: 0.5000, sse=8157728.0, rms=4.61 032: dt: 0.5000, sse=8040018.0, rms=4.47 033: dt: 0.5000, sse=8740012.0, rms=4.32 034: dt: 0.5000, sse=8543644.0, rms=4.23 035: dt: 0.5000, sse=9013625.0, rms=4.14 rms = 4.09, time step reduction 1 of 3 to 0.250... 036: dt: 0.5000, sse=8803428.0, rms=4.09 037: dt: 0.2500, sse=7732754.5, rms=3.81 038: dt: 0.2500, sse=7638658.5, rms=3.72 rms = 3.72, time step reduction 2 of 3 to 0.125... rms = 3.69, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=7572917.5, rms=3.69 positioning took 1.2 minutes mean border=57.4, 2377 (55) missing vertices, mean dist 0.2 [0.3 (%39.2)->0.7 (%60.8))] %48 local maxima, %18 large gradients and %28 min vals, 1788 gradients ignored tol=1.0e-04, sigma=0.5, host=local, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=7720678.5, rms=4.11 040: dt: 0.5000, sse=8137027.5, rms=4.04 041: dt: 0.5000, sse=9343997.0, rms=3.90 rms = 3.95, time step reduction 1 of 3 to 0.250... 042: dt: 0.2500, sse=8482678.0, rms=3.66 043: dt: 0.2500, sse=8124688.0, rms=3.58 rms = 3.56, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=8108353.5, rms=3.56 045: dt: 0.1250, sse=7932442.5, rms=3.49 rms = 3.47, time step reduction 3 of 3 to 0.062... 046: dt: 0.1250, sse=7935019.0, rms=3.47 positioning took 0.8 minutes mean border=56.9, 4673 (50) missing vertices, mean dist 0.1 [0.3 (%42.6)->0.6 (%57.4))] %51 local maxima, %14 large gradients and %27 min vals, 1741 gradients ignored tol=1.0e-04, sigma=0.2, host=local, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=7960574.0, rms=3.56 rms = 3.62, time step reduction 1 of 3 to 0.250... 047: dt: 0.2500, sse=7887867.0, rms=3.47 048: dt: 0.2500, sse=8093015.5, rms=3.41 rms = 3.38, time step reduction 2 of 3 to 0.125... 049: dt: 0.2500, sse=8210099.5, rms=3.38 050: dt: 0.1250, sse=8138982.5, rms=3.31 rms = 3.29, time step reduction 3 of 3 to 0.062... 051: dt: 0.1250, sse=8170343.0, rms=3.29 positioning took 0.6 minutes writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.area.pial vertex spacing 1.08 +- 0.50 (0.03-->9.47) (max @ vno 102662 --> 101707) face area 0.46 +- 0.39 (0.00-->11.88) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 137942 vertices processed 25000 of 137942 vertices processed 50000 of 137942 vertices processed 75000 of 137942 vertices processed 100000 of 137942 vertices processed 125000 of 137942 vertices processed 0 of 137942 vertices processed 25000 of 137942 vertices processed 50000 of 137942 vertices processed 75000 of 137942 vertices processed 100000 of 137942 vertices processed 125000 of 137942 vertices processed thickness calculation complete, 4462:5273 truncations. 43367 vertices at 0 distance 61181 vertices at 1 distance 70657 vertices at 2 distance 48208 vertices at 3 distance 22890 vertices at 4 distance 9603 vertices at 5 distance 3899 vertices at 6 distance 1740 vertices at 7 distance 894 vertices at 8 distance 552 vertices at 9 distance 416 vertices at 10 distance 336 vertices at 11 distance 246 vertices at 12 distance 228 vertices at 13 distance 177 vertices at 14 distance 158 vertices at 15 distance 103 vertices at 16 distance 104 vertices at 17 distance 72 vertices at 18 distance 71 vertices at 19 distance 110 vertices at 20 distance writing curvature file /export/data2/data1/tools/freesurfer/subjects/soo-eun/NF108_11/surf/rh.thickness positioning took 14.5 minutes #-------------------------------------------- #@# Surf Volume rh Tue May 1 00:38:01 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/surf mris_calc -o rh.area.mid rh.area add rh.area.pial mris_calc -o rh.area.mid rh.area.mid div 2 mris_calc -o rh.volume rh.area.mid mul rh.thickness #-------------------------------------------- #@# Smooth2 rh Tue May 1 00:38:01 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /export/data2/PI/ChildStutter/NF108_11/freesurfer/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 Tue May 1 00:38:05 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.2 mm, total surface area = 84740 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.125 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.069 (target=0.015) step 015: RMS=0.058 (target=0.015) step 020: RMS=0.050 (target=0.015) step 025: RMS=0.044 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.030 (target=0.015) step 045: RMS=0.026 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. inflation took 0.9 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 340 vertices thresholded to be in k1 ~ [-0.34 0.28], k2 ~ [-0.12 0.08] total integrated curvature = 0.265*4pi (3.327) --> 1 handles ICI = 1.3, FI = 11.7, variation=187.328 187 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 140 vertices thresholded to be in [-0.18 0.14] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.025 done. #----------------------------------------- #@# Curvature Stats rh Tue May 1 00:40:27 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm NF108_11 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 [ NF108_11/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture... [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 298 ] WARN: S lookup min: -0.013703 WARN: S explicit min: 0.000000 vertex = 155 #-------------------------------------------- #@# Sphere rh Tue May 1 00:40:32 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... writing spherical brain to ../surf/rh.sphere spherical transformation took 1.84 hours scaling brain by 0.279... pass 1: epoch 1 of 3 starting distance error %20.88 pass 1: epoch 2 of 3 starting distance error %20.77 unfolding complete - removing small folds... starting distance error %20.58 removing remaining folds... final distance error %20.58 502: 0 negative triangles #-------------------------------------------- #@# Surf Reg rh Tue May 1 02:30:50 EDT 2012 /export/data2/PI/ChildStutter/NF108_11/freesurfer/scripts mris_register -curv ../surf/rh.sphere /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /export/data1/tools/freesurfer/average/rh.average.curvature.filled.buckner40.tif... New invocation of recon-all Tue Jul 17 17:16:22 EDT 2012 /export/data2/PI/freesurfer_subjects/NF108_11 /export/data1/tools/freesurfer/bin/recon-all -s NF108_11 -qcache subjid NF108_11 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects FREESURFER_HOME /export/data1/tools/freesurfer Actual FREESURFER_HOME /export/data2/data1/tools/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16334248 15753176 581072 0 1685680 10714284 -/+ buffers/cache: 3353212 12981036 Swap: 18579448 1348 18578100 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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 stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:22-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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: stable5 $ TimeStamp: 2012/07/17-21:16:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:23-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/17-21:16:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /export/data1/tools/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /export/data1/tools/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### New invocation of recon-all Thu Jul 26 15:30:00 EDT 2012 /export/data2/PI/freesurfer_subjects/NF108_11 /export/data1/tools/freesurfer/bin/recon-all -s NF108_11 -qcache subjid NF108_11 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects FREESURFER_HOME /export/data1/tools/freesurfer Actual FREESURFER_HOME /export/data2/data1/tools/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16334248 15209208 1125040 0 1426140 10332240 -/+ buffers/cache: 3450828 12883420 Swap: 18579448 14120 18565328 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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 stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 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: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-19:30:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: soo-eun Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.32-131.4.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /export/data1/tools/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /export/data1/tools/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /export/data2/PI/freesurfer_subjects/NF108_11/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Thu Jul 26 15:30:03 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.30120 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Jul 26 15:30:03 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.30120 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:30:03 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.30120/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.30120/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.thickness Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.30120/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.30120/NF108_11.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.30120 Thu Jul 26 15:30:12 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh thickness fwhm0 fsaverage Thu Jul 26 15:30:12 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm5 fsaverage Thu Jul 26 15:30:15 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm10 fsaverage Thu Jul 26 15:30:23 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm15 fsaverage Thu Jul 26 15:30:36 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm20 fsaverage Thu Jul 26 15:30:58 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh thickness fwhm25 fsaverage Thu Jul 26 15:31:32 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fsaverage Thu Jul 26 15:32:26 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.30620 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.area.fsaverage.mris_preproc.log Thu Jul 26 15:32:26 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.30620 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:32:26 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.30620/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.30620/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.30620/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.30620/NF108_11.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.30620 Thu Jul 26 15:32:33 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area fwhm0 fsaverage Thu Jul 26 15:32:33 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm5 fsaverage Thu Jul 26 15:32:36 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm10 fsaverage Thu Jul 26 15:32:44 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm15 fsaverage Thu Jul 26 15:32:58 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm20 fsaverage Thu Jul 26 15:33:19 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area fwhm25 fsaverage Thu Jul 26 15:33:53 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Thu Jul 26 15:34:42 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.31086 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Thu Jul 26 15:34:42 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.31086 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:34:42 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.31086/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area.pial --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.31086/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.area.pial Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.31086/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.31086/NF108_11.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.31086 Thu Jul 26 15:34:50 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm0 fsaverage Thu Jul 26 15:34:50 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm5 fsaverage Thu Jul 26 15:34:53 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm10 fsaverage Thu Jul 26 15:35:01 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm15 fsaverage Thu Jul 26 15:35:14 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm20 fsaverage Thu Jul 26 15:35:36 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm25 fsaverage Thu Jul 26 15:36:10 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Thu Jul 26 15:37:00 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.31567 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.volume.fsaverage.mris_preproc.log Thu Jul 26 15:37:00 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.31567 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:37:00 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.31567/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.31567/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.volume Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.31567/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.31567/NF108_11.1.mgh --o lh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.volume.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.31567 Thu Jul 26 15:37:08 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh volume fwhm0 fsaverage Thu Jul 26 15:37:08 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.volume.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm5 fsaverage Thu Jul 26 15:37:10 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.volume.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm10 fsaverage Thu Jul 26 15:37:18 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.volume.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm15 fsaverage Thu Jul 26 15:37:31 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.volume.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm20 fsaverage Thu Jul 26 15:37:53 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.volume.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh volume fwhm25 fsaverage Thu Jul 26 15:38:27 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.volume.fsaverage.mgh --tval lh.volume.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.volume.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.volume.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.volume.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fsaverage Thu Jul 26 15:39:15 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.32016 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.curv.fsaverage.mris_preproc.log Thu Jul 26 15:39:15 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.32016 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:39:15 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.32016/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.curv --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.32016/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.curv Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.32016/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.32016/NF108_11.1.mgh --o lh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.curv.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.32016 Thu Jul 26 15:39:23 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh curv fwhm0 fsaverage Thu Jul 26 15:39:23 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.curv.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm5 fsaverage Thu Jul 26 15:39:26 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.curv.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm10 fsaverage Thu Jul 26 15:39:34 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.curv.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm15 fsaverage Thu Jul 26 15:39:47 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.curv.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm20 fsaverage Thu Jul 26 15:40:09 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.curv.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh curv fwhm25 fsaverage Thu Jul 26 15:40:43 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.curv.fsaverage.mgh --tval lh.curv.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.curv.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.curv.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.curv.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fsaverage Thu Jul 26 15:41:31 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.32478 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.sulc.fsaverage.mris_preproc.log Thu Jul 26 15:41:32 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.32478 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:41:32 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.32478/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sulc --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.32478/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sulc Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.32478/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.32478/NF108_11.1.mgh --o lh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.sulc.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.32478 Thu Jul 26 15:41:39 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh sulc fwhm0 fsaverage Thu Jul 26 15:41:39 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.sulc.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm5 fsaverage Thu Jul 26 15:41:42 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.sulc.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm10 fsaverage Thu Jul 26 15:41:49 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.sulc.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm15 fsaverage Thu Jul 26 15:42:03 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.sulc.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm20 fsaverage Thu Jul 26 15:42:24 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.sulc.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh sulc fwhm25 fsaverage Thu Jul 26 15:42:58 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.sulc.fsaverage.mgh --tval lh.sulc.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.sulc.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.sulc.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.sulc.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh white.K fsaverage Thu Jul 26 15:43:47 EDT 2012 INFO: File lh.white.K does not exist! Skipping creation of smoothed data for lh.white.K #-------------------------------------------- #@# Qdec Cache lh white.H fsaverage Thu Jul 26 15:43:47 EDT 2012 INFO: File lh.white.H does not exist! Skipping creation of smoothed data for lh.white.H #-------------------------------------------- #@# Qdec Cache lh jacobian_white fsaverage Thu Jul 26 15:43:47 EDT 2012 mris_preproc --s NF108_11 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.548 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is lh.jacobian_white.fsaverage.mris_preproc.log Thu Jul 26 15:43:47 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi lh --meas jacobian_white --target fsaverage --out lh.jacobian_white.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.548 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:43:47 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.548/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.jacobian_white --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.jacobian_white srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.548/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/lh.jacobian_white Reading target surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (140905) Reverse Loop had 29037 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 143099, nTrgMulti = 20743, MnTrgMultiHits = 2.39985 nSrc121 = 102237, nSrcLost = 0, nSrcMulti = 38668, MnSrcMultiHits = 2.34411 Saving target data Saving to ./tmp.mris_preproc.548/NF108_11.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.548/NF108_11.1.mgh --o lh.jacobian_white.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.jacobian_white.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.548 Thu Jul 26 15:43:55 EDT 2012 mris_preproc done #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm0 fsaverage Thu Jul 26 15:43:55 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.jacobian_white.fwhm0.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm5 fsaverage Thu Jul 26 15:43:57 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.jacobian_white.fwhm5.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm10 fsaverage Thu Jul 26 15:44:05 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.jacobian_white.fwhm10.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm15 fsaverage Thu Jul 26 15:44:18 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.jacobian_white.fwhm15.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm20 fsaverage Thu Jul 26 15:44:39 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.jacobian_white.fwhm20.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache lh jacobian_white fwhm25 fsaverage Thu Jul 26 15:45:12 EDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.jacobian_white.fsaverage.mgh --tval lh.jacobian_white.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.jacobian_white.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.jacobian_white.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.jacobian_white.fwhm25.fsaverage.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fsaverage Thu Jul 26 15:46:00 EDT 2012 mris_preproc --s NF108_11 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.801 /export/data2/PI/freesurfer_subjects/NF108_11/surf Log file is rh.thickness.fsaverage.mris_preproc.log Thu Jul 26 15:46:00 EDT 2012 setenv SUBJECTS_DIR /export/data2/PI/freesurfer_subjects cd /export/data2/PI/freesurfer_subjects/NF108_11/surf /export/data1/tools/freesurfer/bin/mris_preproc --s NF108_11 --hemi rh --meas thickness --target fsaverage --out rh.thickness.fsaverage.mgh Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.801 Src rh sphere.reg Trg rh sphere.reg --------------------------------------------------- #@# 1/1 NF108_11 Thu Jul 26 15:46:00 EDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject NF108_11 --srchemi rh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi rh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.801/NF108_11.1.mgh --sval /export/data2/PI/freesurfer_subjects/NF108_11/surf/rh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = NF108_11 srcval = /export/data2/PI/freesurfer_subjects/NF108_11/surf/rh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.801/NF108_11.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /export/data2/PI/freesurfer_subjects/NF108_11/surf/rh.sphere.reg Loading source data Reading curvature file /export/data2/PI/freesurfer_subjects/NF108_11/surf/rh.thickness ERROR: number of vertices in /export/data2/PI/freesurfer_subjects/NF108_11/surf/rh.thickness does not match surface (137942,139279) ERROR: reading curvature file Linux localhost.localdomain 2.6.32-131.4.1.el6.x86_64 #1 SMP Fri Jun 10 10:54:26 EDT 2011 x86_64 x86_64 x86_64 GNU/Linux recon-all -s NF108_11 exited with ERRORS at Thu Jul 26 15:46:02 EDT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting