Mon Oct 15 17:25:51 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 /pkg/brainmap/freesurfer-v4.0.1/bin/recon-all -autorecon1 -subjid 990903_61167 subjid 990903_61167 setenv SUBJECTS_DIR /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE FREESURFER_HOME /pkg/brainmap/freesurfer-v4.0.1 Actual FREESURFER_HOME /pkg/brainmap/freesurfer-v4.0.1 build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v4.0.1 Linux vader 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 78848 ######################################## program versions used $Id: recon-all,v 1.133.2.5 2007/09/17 16:38:00 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7 2007/01/06 00:01:14 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2 $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: tkregister2.c,v 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize.c,v 1.52 2007/01/02 21:34:40 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_watershed.cpp,v 1.67 2007/06/29 13:40:47 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_segment.c,v 1.33 2007/02/14 19:59:27 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_em_register.c,v 1.57 2006/12/29 02:09:06 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_normalize.c,v 1.38 2007/01/02 13:37:33 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_register.c,v 1.63 2007/01/18 22:58:55 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_ca_label.c,v 1.80 2007/04/13 13:22:32 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_inflate.c,v 1.33.2.2 2007/08/16 01:40:10 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_topo_fixer.cpp,v 1.26 2007/02/13 19:30:47 segonne Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_make_surfaces.c,v 1.99 2007/08/14 01:56:01 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mris_anatomical_stats.c,v 1.54 2007/08/02 17:37:13 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2007/10/15-22:25:51-GMT BuildTimeStamp: Sep 18 2007 04:54:49 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2007-08-08.gca GCASkull RB_all_withskull_2007-08-08.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 15 17:25:51 CDT 2007 Found 1 runs /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/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 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig/001.mgz /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/rawavg.mgz /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 mri_convert /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/rawavg.mgz /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig.mgz --conform mri_convert /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/rawavg.mgz /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1.25, 1, 1) mm size and (128, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig.mgz... mri_add_xform_to_header -c /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig.mgz /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 15 17:26:17 CDT 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri /pkg/brainmap/freesurfer-v4.0.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.7 2007/01/06 00:01:14 nicks Exp $ Linux vader 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux Mon Oct 15 17:26:17 CDT 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.22361 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22361/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.22361/nu0.mnc Can't find the talairach xform '/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm' Transform is not loaded into mri $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.22361/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Oct 15 17:26:28 CDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.22361/nu0.mnc ./tmp.mri_nu_correct.mni.22361/nu1.mnc [mharms@vader:/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/] [2007-10-15 17:26:28] running: /pkg/brainmap/freesurfer-v4.0.1/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 /usr/tmp/nu_correct_22409/ ./tmp.mri_nu_correct.mni.22361/nu0.mnc ./tmp.mri_nu_correct.mni.22361/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 50 CV of field change: 0.00166556 [mharms@vader:/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/] [2007-10-15 17:27:32] running: /pkg/brainmap/freesurfer-v4.0.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.22361/nu0.mnc /usr/tmp/nu_correct_22409//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Oct 15 17:27:43 CDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.22361/nu1.mnc ./tmp.mri_nu_correct.mni.22361/nu2.mnc [mharms@vader:/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/] [2007-10-15 17:27:43] running: /pkg/brainmap/freesurfer-v4.0.1/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 /usr/tmp/nu_correct_23090/ ./tmp.mri_nu_correct.mni.22361/nu1.mnc ./tmp.mri_nu_correct.mni.22361/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 50 CV of field change: 0.0010664 [mharms@vader:/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/] [2007-10-15 17:28:49] running: /pkg/brainmap/freesurfer-v4.0.1/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.22361/nu1.mnc /usr/tmp/nu_correct_23090//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_convert ./tmp.mri_nu_correct.mni.22361/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.22361/nu2.mnc nu.mgz --like orig.mgz Can't find the talairach xform '/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm' Transform is not loaded into mri WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from ./tmp.mri_nu_correct.mni.22361/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Mon Oct 15 17:29:18 CDT 2007 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Mon Oct 15 17:29:18 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri /pkg/brainmap/freesurfer-v4.0.1/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.4 2007/05/29 23:24:27 nicks Exp $ Linux vader 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux Mon Oct 15 17:29:19 CDT 2007 -------------------------------------------- mri_convert nu.mgz talsrcimg.img Can't find the talairach xform '/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm' Transform is not loaded into mri $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Mon Oct 15 17:29:25 CDT 2007 /pkg/brainmap/freesurfer-v4.0.1/bin/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.3 2007/08/04 02:23:35 nicks Exp $ target=711-2C_as_mni_average_305 --------------------------------------------------------------------- analyzeto4dfp talsrcimg -O0 -y --------------------------------------------------------------------- $Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Mon Oct 15 17:29:32 2007 Writing: talsrcimg.4dfp.hdr $Id: analyzeto4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.hdr header size 348 bytes hdr.dime.datatype offset=70 value=2 hdr.dime.bitpix offset=72 value=8 hdr.hist.orient offset=252 value=-1 dimensionality 4 dimensions 256 256 256 1 Reading: talsrcimg.img Writing: talsrcimg.4dfp.img Writing: talsrcimg.4dfp.ifh ifh2hdr talsrcimg -r0to255 ori=2 --------------------------------------------------------------------- gauss_4dfp talsrcimg 1.1 --------------------------------------------------------------------- $Id: gauss_4dfp.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.4dfp.img Writing: talsrcimg_g11.4dfp.img image dimensions 256 256 256 padded to 288 288 288 processing volume 1$Id: ifh2hdr.c,v 1.3 2007/05/05 10:45:03 nicks Exp $ Mon Oct 15 17:30:06 2007 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error t4_read: transform initialized to I4 rotation matrix determinant 1.000000 image alignment mode 4355 decimal 1103 hex -7.5000 -45.0000 -45.000010815.5371 11.3044 0.0000 -45.0000 -45.000011345.0078 11.3106 7.5000 -45.0000 -45.000010811.9092 11.2459 -7.5000 -37.5000 -45.000010849.5557 11.3705 0.0000 -37.5000 -45.000011399.0908 11.3814 7.5000 -37.5000 -45.000010829.8467 11.3178 -7.5000 -30.0000 -45.000011181.6670 11.1368 0.0000 -30.0000 -45.000011713.0762 11.1506 7.5000 -30.0000 -45.000011145.6084 11.0881 -7.5000 -22.5000 -45.000011394.4033 10.9271 0.0000 -22.5000 -45.000011945.3506 10.9391 7.5000 -22.5000 -45.000011375.4561 10.8763 -7.5000 -15.0000 -45.000011520.3760 10.7113 0.0000 -15.0000 -45.000012087.9473 10.7188 7.5000 -15.0000 -45.000011497.2676 10.6550 -7.5000 -7.5000 -45.000011573.9844 10.4806 0.0000 -7.5000 -45.000012149.3730 10.4857 7.5000 -7.5000 -45.000011540.6318 10.4219 -7.5000 0.0000 -45.000011565.0459 10.3021 0.0000 0.0000 -45.000012153.4336 10.3087 7.5000 0.0000 -45.000011548.4932 10.2458 -7.5000 7.5000 -45.000010863.2861 10.5192 0.0000 7.5000 -45.000011410.1885 10.5298 7.5000 7.5000 -45.000010867.5420 10.4673 -7.5000 15.0000 -45.000010242.6787 10.8896 0.0000 15.0000 -45.000010776.9482 10.9040 7.5000 15.0000 -45.000010266.5518 10.8408 -7.5000 22.5000 -45.0000 9684.2041 11.3455 0.0000 22.5000 -45.000010170.1748 11.3587 7.5000 22.5000 -45.0000 9695.2363 11.2926 -7.5000 30.0000 -45.0000 9100.2012 11.7153 0.0000 30.0000 -45.0000 9525.9141 11.7233 7.5000 30.0000 -45.0000 9068.8594 11.6530 -7.5000 37.5000 -45.0000 8874.9102 12.1117 0.0000 37.5000 -45.0000 9283.2686 12.1173 7.5000 37.5000 -45.0000 8838.3682 12.0434 -7.5000 45.0000 -45.0000 8305.6475 12.2880 0.0000 45.0000 -45.0000 8702.2246 12.2948 7.5000 45.0000 -45.0000 8280.4424 12.2190 -7.5000 -45.0000 -37.500011303.2109 11.1692 0.0000 -45.0000 -37.500011829.8701 11.1758 7.5000 -45.0000 -37.500011301.6768 11.1140 -7.5000 -37.5000 -37.500011347.7158 11.2361 0.0000 -37.5000 -37.500011889.2158 11.2456 7.5000 -37.5000 -37.500011334.5693 11.1848 -7.5000 -30.0000 -37.500011686.6748 11.0018 0.0000 -30.0000 -37.500012236.8105 11.0121 7.5000 -30.0000 -37.500011651.9434 10.9532 -7.5000 -22.5000 -37.500011894.5957 10.7896 0.0000 -22.5000 -37.500012471.9258 10.7975 7.5000 -22.5000 -37.500011873.5469 10.7389 -7.5000 -15.0000 -37.500012009.0869 10.5739 0.0000 -15.0000 -37.500012595.6914 10.5788 7.5000 -15.0000 -37.500011989.5225 10.5191 -7.5000 -7.5000 -37.500012037.3887 10.3484 0.0000 -7.5000 -37.500012638.9541 10.3531 7.5000 -7.5000 -37.500012014.2578 10.2925 -7.5000 0.0000 -37.500012036.3633 10.1760 0.0000 0.0000 -37.500012629.6816 10.1830 7.5000 0.0000 -37.500012029.3066 10.1226 -7.5000 7.5000 -37.500011279.7949 10.3921 0.0000 7.5000 -37.500011800.4072 10.4016 7.5000 7.5000 -37.500011273.7988 10.3416 -7.5000 15.0000 -37.500010610.4160 10.7557 0.0000 15.0000 -37.500011127.6035 10.7665 7.5000 15.0000 -37.500010606.5557 10.7067 -7.5000 22.5000 -37.5000 9995.5430 11.2019 0.0000 22.5000 -37.500010479.9336 11.2103 7.5000 22.5000 -37.5000 9992.8301 11.1486 -7.5000 30.0000 -37.5000 9358.7822 11.5675 0.0000 30.0000 -37.5000 9783.8887 11.5720 7.5000 30.0000 -37.5000 9342.3516 11.5061 -7.5000 37.5000 -37.5000 9146.9541 11.9632 0.0000 37.5000 -37.5000 9553.0176 11.9679 7.5000 37.5000 -37.5000 9115.8281 11.8973 -7.5000 45.0000 -37.5000 8538.8320 12.1442 0.0000 45.0000 -37.5000 8913.5000 12.1509 7.5000 45.0000 -37.5000 8519.3018 12.0774 -7.5000 -45.0000 -30.000012094.1348 11.4008 0.0000 -45.0000 -30.000012657.2861 11.4089 7.5000 -45.0000 -30.000012087.4102 11.3441 -7.5000 -37.5000 -30.000012127.0664 11.4732 0.0000 -37.5000 -30.000012694.4502 11.4820 7.5000 -37.5000 -30.000012108.3291 11.4166 -7.5000 -30.0000 -30.000012474.3096 11.2312 0.0000 -30.0000 -30.000013061.9502 11.2393 7.5000 -30.0000 -30.000012448.9326 11.1760 -7.5000 -22.5000 -30.000012684.8848 11.0069 0.0000 -22.5000 -30.000013327.1201 11.0134 7.5000 -22.5000 -30.000012679.7646 10.9526 -7.5000 -15.0000 -30.000012801.1318 10.7798 0.0000 -15.0000 -30.000013454.9648 10.7853 7.5000 -15.0000 -30.000012797.4492 10.7248 -7.5000 -7.5000 -30.000012851.7295 10.5481 0.0000 -7.5000 -30.000013483.4873 10.5547 7.5000 -7.5000 -30.000012823.1357 10.4928 -7.5000 0.0000 -30.000012836.2197 10.3750 0.0000 0.0000 -30.000013449.3564 10.3834 7.5000 0.0000 -30.000012825.9307 10.3204 -7.5000 7.5000 -30.000012009.9668 10.6007 0.0000 7.5000 -30.000012556.5703 10.6096 7.5000 7.5000 -30.000011997.1328 10.5456 -7.5000 15.0000 -30.000011285.1533 10.9735 0.0000 15.0000 -30.000011795.2412 10.9820 7.5000 15.0000 -30.000011276.3203 10.9178 -7.5000 22.5000 -30.000010603.7334 11.4234 0.0000 22.5000 -30.000011105.1709 11.4301 7.5000 22.5000 -30.000010588.9375 11.3659 -7.5000 30.0000 -30.0000 9911.0557 11.7963 0.0000 30.0000 -30.000010376.0234 11.8015 7.5000 30.0000 -30.0000 9897.0693 11.7344 -7.5000 37.5000 -30.0000 9672.9492 12.2002 0.0000 37.5000 -30.000010106.3809 12.2067 7.5000 37.5000 -30.0000 9650.6660 12.1338 -7.5000 45.0000 -30.0000 9044.8906 12.3980 0.0000 45.0000 -30.0000 9430.5488 12.4062 7.5000 45.0000 -30.0000 9027.7871 12.3281 -7.5000 -45.0000 -22.500012873.3213 11.5824 0.0000 -45.0000 -22.500013502.1504 11.5911 7.5000 -45.0000 -22.500012870.0244 11.5226 -7.5000 -37.5000 -22.500012913.2705 11.6572 0.0000 -37.5000 -22.500013505.8555 11.6663 7.5000 -37.5000 -22.500012891.3115 11.5959 -7.5000 -30.0000 -22.500013285.8916 11.4111 0.0000 -30.0000 -22.500013920.4170 11.4203 7.5000 -30.0000 -22.500013250.7422 11.3515 -7.5000 -22.5000 -22.500013519.6562 11.1808 0.0000 -22.5000 -22.500014219.9463 11.1899 7.5000 -22.5000 -22.500013512.6768 11.1245 -7.5000 -15.0000 -22.500013646.5938 10.9458 0.0000 -15.0000 -22.500014340.5439 10.9542 7.5000 -15.0000 -22.500013646.5977 10.8905 -7.5000 -7.5000 -22.500013673.7158 10.7065 0.0000 -7.5000 -22.500014344.9404 10.7148 7.5000 -7.5000 -22.500013651.7852 10.6501 -7.5000 0.0000 -22.500013663.3066 10.5290 0.0000 0.0000 -22.500014312.1680 10.5380 7.5000 0.0000 -22.500013650.8291 10.4717 -7.5000 7.5000 -22.500012763.6729 10.7609 0.0000 7.5000 -22.500013361.3135 10.7701 7.5000 7.5000 -22.500012772.7002 10.7018 -7.5000 15.0000 -22.500011977.4727 11.1430 0.0000 15.0000 -22.500012544.0088 11.1525 7.5000 15.0000 -22.500011978.0410 11.0833 -7.5000 22.5000 -22.500011242.0088 11.5992 0.0000 22.5000 -22.500011788.6865 11.6088 7.5000 22.5000 -22.500011251.2715 11.5401 -7.5000 30.0000 -22.500010500.8516 11.9780 0.0000 30.0000 -22.500011003.1201 11.9871 7.5000 30.0000 -22.500010486.2520 11.9165 -7.5000 37.5000 -22.500010233.6348 12.3875 0.0000 37.5000 -22.500010698.1553 12.3960 7.5000 37.5000 -22.500010203.7539 12.3196 -7.5000 45.0000 -22.5000 9553.3438 12.5961 0.0000 45.0000 -22.5000 9978.5732 12.6048 7.5000 45.0000 -22.5000 9538.8848 12.5222 -7.5000 -45.0000 -15.000013744.1631 11.7087 0.0000 -45.0000 -15.000014404.2256 11.7182 7.5000 -45.0000 -15.000013742.5264 11.6470 -7.5000 -37.5000 -15.000013800.8281 11.7806 0.0000 -37.5000 -15.000014427.1367 11.7922 7.5000 -37.5000 -15.000013781.8213 11.7197 -7.5000 -30.0000 -15.000014190.2861 11.5303 0.0000 -30.0000 -15.000014918.7217 11.5439 7.5000 -30.0000 -15.000014195.8477 11.4723 -7.5000 -22.5000 -15.000014420.0186 11.2990 0.0000 -22.5000 -15.000015214.1621 11.3126 7.5000 -22.5000 -15.000014445.0811 11.2436 -7.5000 -15.0000 -15.000014514.4424 11.0613 0.0000 -15.0000 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45.0000 45.0000 8381.5889 14.1034 --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: 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30.0000 2887.7632 13.2395 7.5000 -45.0000 30.0000 2889.9497 13.3931 -7.5000 -37.5000 30.0000 2876.8206 13.6966 0.0000 -37.5000 30.0000 2888.4751 13.5381 7.5000 -37.5000 30.0000 2881.6179 13.6897 -7.5000 -30.0000 30.0000 2856.8054 13.9991 0.0000 -30.0000 30.0000 2872.3240 13.8251 7.5000 -30.0000 30.0000 2856.1812 13.9966 -7.5000 -22.5000 30.0000 2838.2961 14.4511 0.0000 -22.5000 30.0000 2856.1328 14.2927 7.5000 -22.5000 30.0000 2842.2827 14.4312 -7.5000 -15.0000 30.0000 2813.0469 15.0236 0.0000 -15.0000 30.0000 2830.0183 14.8656 7.5000 -15.0000 30.0000 2819.0669 14.9698 -7.5000 -7.5000 30.0000 2778.0662 15.6100 0.0000 -7.5000 30.0000 2793.1697 15.4645 7.5000 -7.5000 30.0000 2777.7117 15.5406 -7.5000 0.0000 30.0000 2724.5105 16.2435 0.0000 0.0000 30.0000 2738.4705 16.1046 7.5000 0.0000 30.0000 2725.0100 16.1526 -7.5000 7.5000 30.0000 2678.5122 16.9775 0.0000 7.5000 30.0000 2697.1370 16.8039 7.5000 7.5000 30.0000 2682.6001 16.8625 -7.5000 15.0000 30.0000 2613.5662 17.9052 0.0000 15.0000 30.0000 2634.1667 17.7335 7.5000 15.0000 30.0000 2618.1260 17.8091 -7.5000 22.5000 30.0000 2544.4919 18.9676 0.0000 22.5000 30.0000 2560.9148 18.8422 7.5000 22.5000 30.0000 2545.5491 18.9129 -7.5000 30.0000 30.0000 2483.8782 20.2121 0.0000 30.0000 30.0000 2500.2649 20.1381 7.5000 30.0000 30.0000 2489.0037 20.1764 -7.5000 37.5000 30.0000 2462.9438 21.6524 0.0000 37.5000 30.0000 2472.6716 21.4761 7.5000 37.5000 30.0000 2459.9888 21.5679 -7.5000 -52.5000 37.5000 2851.2888 13.5923 0.0000 -52.5000 37.5000 2850.6223 13.3117 7.5000 -52.5000 37.5000 2850.8877 13.4661 -7.5000 -45.0000 37.5000 2847.5725 13.7542 0.0000 -45.0000 37.5000 2846.9490 13.5034 7.5000 -45.0000 37.5000 2847.7986 13.6545 -7.5000 -37.5000 37.5000 2842.5701 14.0075 0.0000 -37.5000 37.5000 2842.2114 13.7794 7.5000 -37.5000 37.5000 2840.1511 13.9524 -7.5000 -30.0000 37.5000 2818.1536 14.3424 0.0000 -30.0000 37.5000 2822.8381 14.1505 7.5000 -30.0000 37.5000 2819.0195 14.3273 -7.5000 -22.5000 37.5000 2798.3455 14.8812 0.0000 -22.5000 37.5000 2810.8945 14.6927 7.5000 -22.5000 37.5000 2799.7744 14.8316 -7.5000 -15.0000 37.5000 2770.9434 15.5021 0.0000 -15.0000 37.5000 2780.6428 15.3212 7.5000 -15.0000 37.5000 2774.8140 15.4075 -7.5000 -7.5000 37.5000 2739.4373 16.0987 0.0000 -7.5000 37.5000 2750.3149 15.9128 7.5000 -7.5000 37.5000 2738.3472 15.9916 -7.5000 0.0000 37.5000 2688.3384 16.7071 0.0000 0.0000 37.5000 2709.5432 16.5420 7.5000 0.0000 37.5000 2692.2920 16.5717 -7.5000 7.5000 37.5000 2643.3230 17.5016 0.0000 7.5000 37.5000 2662.5374 17.2651 7.5000 7.5000 37.5000 2644.9055 17.3162 -7.5000 15.0000 37.5000 2575.2798 18.4140 0.0000 15.0000 37.5000 2598.5044 18.2018 7.5000 15.0000 37.5000 2577.0242 18.2535 -7.5000 22.5000 37.5000 2516.8496 19.4460 0.0000 22.5000 37.5000 2530.3000 19.3001 7.5000 22.5000 37.5000 2518.1772 19.3745 -7.5000 30.0000 37.5000 2474.3186 20.7150 0.0000 30.0000 37.5000 2486.0342 20.5619 7.5000 30.0000 37.5000 2476.8103 20.6472 -7.5000 37.5000 37.5000 2453.0884 22.0590 0.0000 37.5000 37.5000 2468.9478 21.9063 7.5000 37.5000 37.5000 2459.6477 21.9962 -7.5000 -52.5000 45.0000 2813.4082 14.0287 0.0000 -52.5000 45.0000 2810.5583 13.6915 7.5000 -52.5000 45.0000 2812.8945 13.8303 -7.5000 -45.0000 45.0000 2800.1152 14.1343 0.0000 -45.0000 45.0000 2803.1772 13.8500 7.5000 -45.0000 45.0000 2804.6829 14.0154 -7.5000 -37.5000 45.0000 2785.5237 14.3857 0.0000 -37.5000 45.0000 2788.8711 14.1436 7.5000 -37.5000 45.0000 2794.2771 14.3318 -7.5000 -30.0000 45.0000 2767.1724 14.7588 0.0000 -30.0000 45.0000 2775.4995 14.5625 7.5000 -30.0000 45.0000 2773.6228 14.7177 -7.5000 -22.5000 45.0000 2748.9731 15.3837 0.0000 -22.5000 45.0000 2762.5654 15.1728 7.5000 -22.5000 45.0000 2762.0344 15.3185 -7.5000 -15.0000 45.0000 2722.1636 16.0519 0.0000 -15.0000 45.0000 2730.4880 15.8464 7.5000 -15.0000 45.0000 2731.8611 15.9765 -7.5000 -7.5000 45.0000 2687.4636 16.6782 0.0000 -7.5000 45.0000 2705.1582 16.4849 7.5000 -7.5000 45.0000 2699.7161 16.5780 -7.5000 0.0000 45.0000 2642.0735 17.3197 0.0000 0.0000 45.0000 2670.1116 17.1546 7.5000 0.0000 45.0000 2658.5493 17.1733 -7.5000 7.5000 45.0000 2596.7834 18.1171 0.0000 7.5000 45.0000 2614.2827 17.8903 7.5000 7.5000 45.0000 2604.1162 17.9473 -7.5000 15.0000 45.0000 2530.4294 19.0121 0.0000 15.0000 45.0000 2555.4563 18.7899 7.5000 15.0000 45.0000 2539.4856 18.8701 -7.5000 22.5000 45.0000 2490.5820 20.1688 0.0000 22.5000 45.0000 2500.1592 19.9902 7.5000 22.5000 45.0000 2494.4036 20.0687 -7.5000 30.0000 45.0000 2451.9136 21.3157 0.0000 30.0000 45.0000 2461.4678 21.1755 7.5000 30.0000 45.0000 2451.2090 21.2280 -7.5000 37.5000 45.0000 2431.3418 22.6424 0.0000 37.5000 45.0000 2448.5396 22.5095 7.5000 37.5000 45.0000 2437.4919 22.5650 --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 rotation matrix determinant 1.000000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 1283 decimal 503 hex parameters 0.0000 -37.5000 7.5000 0.0000 0.0000 0.0000 eta,q 0.93529 13.52766 niter,ni,del,rscale 5 3 12.0000 1.2000 parameter 2 -0.760640 -> -0.500000 qaram 1.1500 parameter 4 -9.037804 -> 0.500000 qaram 1.1500 parameters 0.8580 -34.0500 6.7769 -3.4500 -0.0150 -0.9620 eta,q 0.93621 13.37933 0.0855 0.0729 0.0676 0.0643 0.0701 0.0661 0.0789 0.0698 0.0664 0.0642 0.0678 0.0645 0.0720 0.0683 0.0657 0.0643 0.0656 0.0638 0.0683 0.0678 0.0657 0.0658 0.0642 0.0642 0.0686 0.0660 0.0659 0.0677 0.0637 0.0651 0.0723 0.0652 0.0671 0.0679 0.0662 0.0658 0.0789 0.0661 0.0692 0.0673 0.0719 0.0674 niter,ni,del,rscale 6 3 12.0000 1.2000 parameter 4 1.901731 -> 0.500000 qaram 1.3225 parameters 0.6586 -33.7069 6.8389 -7.4175 0.4894 -1.7856 eta,q 0.93676 13.40946 0.0798 0.0724 0.0690 0.0613 0.0684 0.0639 0.0720 0.0665 0.0655 0.0629 0.0655 0.0637 0.0661 0.0636 0.0635 0.0638 0.0646 0.0635 0.0638 0.0638 0.0639 0.0639 0.0633 0.0629 0.0667 0.0638 0.0650 0.0647 0.0622 0.0628 0.0741 0.0650 0.0659 0.0670 0.0636 0.0638 0.0815 0.0707 0.0679 0.0686 0.0678 0.0657 niter,ni,del,rscale 6 3 12.0000 1.2000 parameter 4 0.628456 -> 0.500000 qaram 1.5209 parameters 0.6130 -30.6490 6.6441 -11.9801 0.1412 1.1081 eta,q 0.94530 13.57827 0.0773 0.0734 0.0667 0.0581 0.0619 0.0665 0.0701 0.0679 0.0619 0.0569 0.0592 0.0630 0.0651 0.0651 0.0595 0.0570 0.0575 0.0598 0.0632 0.0633 0.0588 0.0589 0.0567 0.0568 0.0650 0.0597 0.0601 0.0617 0.0573 0.0547 0.0707 0.0584 0.0634 0.0661 0.0597 0.0553 0.0776 0.0640 0.0671 0.0693 0.0639 0.0575 niter,ni,del,rscale 6 3 12.0000 1.2000 parameters 0.9250 -30.7055 5.4975 -13.2351 -0.1468 1.2164 eta,q 0.94653 13.48652 0.0763 0.0712 0.0594 0.0604 0.0608 0.0613 0.0671 0.0640 0.0553 0.0573 0.0577 0.0579 0.0583 0.0572 0.0537 0.0542 0.0549 0.0551 0.0547 0.0547 0.0547 0.0539 0.0534 0.0535 0.0571 0.0561 0.0565 0.0567 0.0542 0.0544 0.0639 0.0637 0.0597 0.0599 0.0576 0.0575 0.0726 0.0726 0.0642 0.0651 0.0637 0.0610 niter,ni,del,rscale 5 3 12.0000 1.2000 parameters 0.9270 -30.6514 5.3342 -13.6055 -0.1717 1.3316 eta,q 0.94669 13.46097 0.0735 0.0709 0.0622 0.0613 0.0613 0.0612 0.0635 0.0635 0.0558 0.0583 0.0580 0.0578 0.0558 0.0562 0.0530 0.0555 0.0552 0.0549 0.0535 0.0535 0.0535 0.0533 0.0533 0.0533 0.0571 0.0552 0.0558 0.0555 0.0537 0.0542 0.0644 0.0617 0.0579 0.0584 0.0568 0.0573 0.0724 0.0716 0.0612 0.0633 0.0628 0.0608 niter,ni,del,rscale 4 3 12.0000 1.2000 parameters 0.9054 -30.6019 5.2250 -13.7363 -0.1421 1.3862 eta,q 0.94683 13.45050 0.0731 0.0708 0.0625 0.0615 0.0614 0.0609 0.0630 0.0633 0.0558 0.0586 0.0581 0.0575 0.0555 0.0559 0.0529 0.0557 0.0551 0.0546 0.0533 0.0533 0.0533 0.0532 0.0532 0.0532 0.0570 0.0551 0.0559 0.0551 0.0536 0.0542 0.0643 0.0615 0.0580 0.0581 0.0566 0.0573 0.0721 0.0715 0.0609 0.0628 0.0626 0.0608 niter,ni,del,rscale 3 3 12.0000 1.2000 parameters 0.8722 -30.5840 5.2034 -13.7826 -0.0993 1.4131 eta,q 0.94688 13.44774 0.0730 0.0707 0.0628 0.0616 0.0615 0.0608 0.0628 0.0631 0.0559 0.0587 0.0581 0.0574 0.0553 0.0557 0.0529 0.0558 0.0551 0.0545 0.0532 0.0532 0.0532 0.0531 0.0531 0.0531 0.0570 0.0551 0.0558 0.0549 0.0535 0.0542 0.0643 0.0615 0.0580 0.0579 0.0566 0.0574 0.0721 0.0716 0.0607 0.0627 0.0626 0.0608 registration optimization eta report parameter search radius 6.0000 6.9000 6.0000 9.1253 6.0000 6.0000 100000*second partial in parameter space 52. 37. 23. 10. 24. 21. 0.0730 0.0707 0.0628 0.0616 0.0615 0.0608 0.0628 0.0631 0.0559 0.0587 0.0581 0.0574 0.0553 0.0557 0.0529 0.0558 0.0551 0.0545 0.0532 0.0532 0.0532 0.0531 0.0531 0.0531 0.0570 0.0551 0.0558 0.0549 0.0535 0.0542 0.0643 0.0615 0.0580 0.0579 0.0566 0.0574 0.0721 0.0716 0.0607 0.0627 0.0626 0.0608 0.8722 -30.5840 5.2034 -13.7826 -0.0993 1.4131 eta,q 0.94688 13.44774 --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 3335 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 3335 decimal D07 hex parameters 0.8722 -30.5840 5.2034 -0.0306 -2.9099 -2.8795 -2.4364 -0.4193 2.4662 23.8207 -0.1733 -23.8238 eta,q 0.94352 13.50315 niter,ni,del,rscale 5 3 5.0000 1.2000 parameter 4 0.946768 -> 0.500000 qaram 1.1500 parameter 5 1.638706 -> 0.500000 qaram 1.1500 parameter 10 0.737990 -> 0.500000 qaram 1.1500 parameters 0.8333 -30.0704 4.9531 -4.1706 -7.0499 -6.0661 -1.6314 0.2305 1.2017 19.6807 -1.2081 -22.0347 eta,q 0.95254 13.58324 0.0597 0.0587 0.0577 0.0524 0.0472 0.0490 0.0515 0.0530 0.0497 0.0477 0.0481 0.0491 0.0580 0.0576 0.0570 0.0526 0.0484 0.0487 0.0501 0.0506 0.0489 0.0475 0.0477 0.0483 0.0569 0.0569 0.0566 0.0539 0.0502 0.0487 0.0491 0.0493 0.0486 0.0478 0.0475 0.0478 0.0565 0.0565 0.0564 0.0564 0.0528 0.0488 0.0487 0.0487 0.0486 0.0486 0.0475 0.0475 0.0568 0.0565 0.0567 0.0605 0.0561 0.0502 0.0488 0.0488 0.0490 0.0498 0.0477 0.0475 0.0580 0.0567 0.0574 0.0655 0.0600 0.0547 0.0494 0.0497 0.0497 0.0514 0.0480 0.0477 0.0600 0.0574 0.0584 0.0705 0.0637 0.0597 0.0505 0.0517 0.0507 0.0533 0.0484 0.0480 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 3 2.928569 -> 0.500000 qaram 1.1500 parameter 5 0.720819 -> 0.500000 qaram 1.3225 parameters 1.1456 -29.1793 3.5731 -6.2632 -11.8109 -8.4723 -1.3409 0.8527 1.5181 20.9698 -0.6754 -20.2430 eta,q 0.95701 13.48566 0.0509 0.0504 0.0442 0.0478 0.0432 0.0436 0.0456 0.0463 0.0449 0.0461 0.0438 0.0441 0.0493 0.0491 0.0448 0.0463 0.0430 0.0433 0.0444 0.0447 0.0440 0.0448 0.0435 0.0437 0.0481 0.0481 0.0458 0.0452 0.0436 0.0432 0.0435 0.0438 0.0434 0.0437 0.0432 0.0434 0.0475 0.0474 0.0471 0.0451 0.0451 0.0431 0.0432 0.0432 0.0432 0.0432 0.0431 0.0431 0.0475 0.0471 0.0485 0.0464 0.0480 0.0435 0.0434 0.0433 0.0433 0.0432 0.0431 0.0430 0.0482 0.0473 0.0499 0.0497 0.0520 0.0451 0.0441 0.0441 0.0438 0.0437 0.0433 0.0431 0.0496 0.0479 0.0513 0.0552 0.0565 0.0484 0.0453 0.0454 0.0446 0.0448 0.0437 0.0435 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 2 -0.913880 -> -0.500000 qaram 1.1500 parameter 3 1.989805 -> 0.500000 qaram 1.3225 parameters 1.2414 -27.7993 1.9861 -5.5332 -15.7903 -10.9268 -1.7520 0.9074 1.7329 23.9515 -0.6397 -23.1856 eta,q 0.96227 13.46619 0.0457 0.0477 0.0386 0.0449 0.0401 0.0391 0.0405 0.0414 0.0399 0.0425 0.0387 0.0381 0.0443 0.0458 0.0394 0.0428 0.0390 0.0384 0.0393 0.0399 0.0391 0.0407 0.0383 0.0378 0.0434 0.0442 0.0405 0.0409 0.0388 0.0383 0.0385 0.0388 0.0385 0.0393 0.0380 0.0377 0.0430 0.0430 0.0418 0.0397 0.0395 0.0387 0.0383 0.0383 0.0383 0.0383 0.0379 0.0379 0.0432 0.0422 0.0434 0.0394 0.0412 0.0390 0.0387 0.0387 0.0385 0.0379 0.0380 0.0382 0.0440 0.0417 0.0452 0.0406 0.0446 0.0401 0.0396 0.0397 0.0389 0.0382 0.0383 0.0388 0.0454 0.0416 0.0472 0.0441 0.0495 0.0429 0.0410 0.0414 0.0398 0.0391 0.0387 0.0396 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 2 -0.762564 -> -0.500000 qaram 1.3225 parameter 3 1.364995 -> 0.500000 qaram 1.5209 parameter 10 -0.757865 -> -0.500000 qaram 1.3225 parameter 12 0.510918 -> 0.500000 qaram 1.1500 parameters 1.2278 -26.2123 0.1611 -4.9261 -18.7626 -12.6639 -1.8956 0.8444 2.3231 28.7125 -0.4375 -27.3256 eta,q 0.96841 13.54042 0.0407 0.0442 0.0333 0.0395 0.0354 0.0346 0.0358 0.0367 0.0350 0.0389 0.0330 0.0319 0.0391 0.0416 0.0337 0.0372 0.0340 0.0337 0.0343 0.0349 0.0341 0.0365 0.0324 0.0316 0.0381 0.0394 0.0347 0.0353 0.0333 0.0332 0.0335 0.0337 0.0335 0.0347 0.0320 0.0316 0.0377 0.0377 0.0363 0.0339 0.0337 0.0333 0.0332 0.0332 0.0332 0.0332 0.0319 0.0319 0.0381 0.0367 0.0385 0.0335 0.0351 0.0338 0.0335 0.0337 0.0333 0.0322 0.0320 0.0324 0.0392 0.0363 0.0407 0.0350 0.0378 0.0351 0.0345 0.0349 0.0337 0.0318 0.0323 0.0332 0.0408 0.0364 0.0431 0.0391 0.0425 0.0377 0.0360 0.0369 0.0345 0.0320 0.0328 0.0341 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 2 -0.524549 -> -0.500000 qaram 1.5209 parameter 3 0.851402 -> 0.500000 qaram 1.7490 parameter 10 -1.075353 -> -0.500000 qaram 1.5209 parameters 1.1048 -24.3873 -1.9377 -4.9380 -22.0132 -15.1631 -1.6435 0.3839 2.2936 34.1876 -0.8322 -29.3052 eta,q 0.97615 13.61413 0.0348 0.0394 0.0281 0.0340 0.0297 0.0282 0.0302 0.0307 0.0288 0.0358 0.0254 0.0254 0.0330 0.0361 0.0279 0.0315 0.0281 0.0274 0.0286 0.0286 0.0279 0.0325 0.0245 0.0243 0.0319 0.0334 0.0288 0.0294 0.0274 0.0271 0.0275 0.0274 0.0273 0.0297 0.0241 0.0239 0.0316 0.0316 0.0305 0.0281 0.0281 0.0274 0.0271 0.0271 0.0271 0.0271 0.0241 0.0240 0.0322 0.0306 0.0332 0.0280 0.0299 0.0283 0.0273 0.0278 0.0273 0.0251 0.0243 0.0248 0.0335 0.0306 0.0366 0.0303 0.0329 0.0309 0.0283 0.0293 0.0279 0.0238 0.0248 0.0260 0.0355 0.0315 0.0403 0.0353 0.0381 0.0358 0.0298 0.0317 0.0289 0.0240 0.0257 0.0274 niter,ni,del,rscale 7 3 5.0000 1.2000 parameters 0.9541 -23.1646 -3.3608 -4.7538 -23.8494 -16.9423 -1.5010 0.3079 2.0442 37.5274 -1.1002 -31.7095 eta,q 0.97968 13.68293 0.0274 0.0348 0.0254 0.0287 0.0260 0.0240 0.0253 0.0270 0.0241 0.0326 0.0221 0.0218 0.0253 0.0301 0.0230 0.0260 0.0236 0.0227 0.0235 0.0241 0.0229 0.0283 0.0212 0.0207 0.0241 0.0263 0.0221 0.0238 0.0221 0.0220 0.0224 0.0225 0.0221 0.0246 0.0207 0.0203 0.0238 0.0238 0.0230 0.0221 0.0221 0.0219 0.0219 0.0219 0.0219 0.0219 0.0206 0.0206 0.0245 0.0230 0.0256 0.0219 0.0237 0.0226 0.0222 0.0225 0.0222 0.0205 0.0208 0.0215 0.0260 0.0238 0.0297 0.0243 0.0266 0.0253 0.0233 0.0242 0.0231 0.0213 0.0215 0.0229 0.0284 0.0263 0.0350 0.0295 0.0311 0.0305 0.0251 0.0273 0.0245 0.0252 0.0224 0.0247 niter,ni,del,rscale 6 3 5.0000 1.2000 parameters 0.9328 -22.7494 -3.8142 -4.5846 -24.7446 -17.6033 -1.3723 0.2602 1.9560 37.9853 -1.1476 -32.5542 eta,q 0.97997 13.69201 0.0246 0.0300 0.0261 0.0268 0.0254 0.0238 0.0237 0.0261 0.0229 0.0291 0.0217 0.0223 0.0223 0.0253 0.0226 0.0241 0.0226 0.0219 0.0219 0.0227 0.0214 0.0250 0.0208 0.0209 0.0208 0.0220 0.0206 0.0218 0.0207 0.0207 0.0206 0.0208 0.0205 0.0220 0.0202 0.0202 0.0203 0.0203 0.0202 0.0201 0.0200 0.0200 0.0202 0.0202 0.0202 0.0202 0.0201 0.0201 0.0208 0.0205 0.0215 0.0199 0.0212 0.0202 0.0205 0.0209 0.0205 0.0201 0.0203 0.0206 0.0223 0.0227 0.0247 0.0224 0.0241 0.0223 0.0217 0.0228 0.0215 0.0230 0.0208 0.0217 0.0248 0.0266 0.0296 0.0277 0.0281 0.0268 0.0235 0.0262 0.0230 0.0288 0.0217 0.0233 niter,ni,del,rscale 5 3 5.0000 1.2000 parameters 0.9175 -22.6180 -3.9018 -4.4328 -25.0023 -17.6737 -1.3594 0.2699 1.9065 38.2083 -1.1961 -32.8096 eta,q 0.98006 13.70058 0.0243 0.0285 0.0270 0.0266 0.0260 0.0243 0.0235 0.0262 0.0227 0.0287 0.0216 0.0226 0.0220 0.0242 0.0233 0.0240 0.0232 0.0222 0.0216 0.0226 0.0213 0.0247 0.0207 0.0210 0.0205 0.0213 0.0209 0.0216 0.0210 0.0208 0.0204 0.0206 0.0203 0.0217 0.0201 0.0202 0.0200 0.0200 0.0200 0.0200 0.0200 0.0200 0.0200 0.0200 0.0200 0.0200 0.0199 0.0199 0.0205 0.0207 0.0208 0.0198 0.0207 0.0198 0.0204 0.0207 0.0203 0.0201 0.0202 0.0204 0.0220 0.0233 0.0234 0.0223 0.0233 0.0214 0.0216 0.0226 0.0213 0.0232 0.0207 0.0214 0.0245 0.0275 0.0279 0.0275 0.0271 0.0255 0.0235 0.0261 0.0228 0.0291 0.0216 0.0229 niter,ni,del,rscale 4 3 5.0000 1.2000 parameters 0.9112 -22.5826 -3.9313 -4.4121 -25.0896 -17.6995 -1.3552 0.2758 1.8962 38.2800 -1.2151 -32.8975 eta,q 0.98007 13.70224 0.0243 0.0281 0.0271 0.0265 0.0262 0.0243 0.0234 0.0262 0.0227 0.0285 0.0216 0.0227 0.0219 0.0238 0.0233 0.0238 0.0233 0.0223 0.0215 0.0226 0.0213 0.0245 0.0206 0.0211 0.0205 0.0210 0.0209 0.0215 0.0210 0.0208 0.0204 0.0206 0.0203 0.0216 0.0201 0.0202 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0204 0.0208 0.0207 0.0198 0.0206 0.0197 0.0203 0.0206 0.0203 0.0201 0.0201 0.0203 0.0219 0.0236 0.0232 0.0225 0.0231 0.0213 0.0215 0.0226 0.0212 0.0234 0.0207 0.0213 0.0244 0.0278 0.0276 0.0278 0.0268 0.0254 0.0235 0.0261 0.0228 0.0294 0.0216 0.0227 niter,ni,del,rscale 3 3 5.0000 1.2000 parameters 0.9104 -22.5715 -3.9405 -4.4057 -25.1186 -17.7062 -1.3519 0.2784 1.8912 38.3058 -1.2230 -32.9274 eta,q 0.98008 13.70281 0.0243 0.0280 0.0272 0.0264 0.0262 0.0243 0.0234 0.0262 0.0227 0.0285 0.0216 0.0227 0.0219 0.0237 0.0234 0.0238 0.0233 0.0223 0.0215 0.0226 0.0212 0.0245 0.0207 0.0211 0.0205 0.0210 0.0209 0.0215 0.0211 0.0208 0.0204 0.0205 0.0203 0.0216 0.0201 0.0202 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0204 0.0209 0.0206 0.0198 0.0205 0.0197 0.0203 0.0206 0.0203 0.0202 0.0201 0.0203 0.0219 0.0236 0.0232 0.0225 0.0230 0.0213 0.0215 0.0226 0.0212 0.0234 0.0207 0.0212 0.0244 0.0279 0.0275 0.0278 0.0267 0.0254 0.0234 0.0261 0.0228 0.0295 0.0216 0.0227 registration optimization eta report parameter search radius 2.4000 3.6501 4.1976 8.2800 9.5220 7.2000 7.2000 7.2000 7.2000 10.9503 7.2000 8.2800 100000*second partial in parameter space 76. 60. 42. 11. 7. 10. 7. 12. 5. 8. 3. 4. 0.0243 0.0280 0.0272 0.0264 0.0262 0.0243 0.0234 0.0262 0.0227 0.0285 0.0216 0.0227 0.0219 0.0237 0.0234 0.0238 0.0233 0.0223 0.0215 0.0226 0.0212 0.0245 0.0207 0.0211 0.0205 0.0210 0.0209 0.0215 0.0211 0.0208 0.0204 0.0205 0.0203 0.0216 0.0201 0.0202 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0199 0.0204 0.0209 0.0206 0.0198 0.0205 0.0197 0.0203 0.0206 0.0203 0.0202 0.0201 0.0203 0.0219 0.0236 0.0232 0.0225 0.0230 0.0213 0.0215 0.0226 0.0212 0.0234 0.0207 0.0212 0.0244 0.0279 0.0275 0.0278 0.0267 0.0254 0.0234 0.0261 0.0228 0.0295 0.0216 0.0227 0.9104 -22.5715 -3.9405 -4.4057 -25.1186 -17.7062 -1.3519 0.2784 1.8912 38.3058 -1.2230 -32.9274 eta,q 0.98008 13.70281 --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 2311 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 2311 decimal 907 hex parameters 0.9104 -22.5715 -3.9405 -4.4057 -25.1186 -17.7062 -1.3519 0.2784 1.8912 38.3058 -1.2230 -32.9274 eta,q 0.98008 13.70280 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters 0.9275 -22.5556 -3.8369 -3.3769 -24.9310 -17.0516 -1.4412 0.3268 1.7925 39.1779 -1.3746 -33.0931 eta,q 0.98065 13.75125 0.0219 0.0216 0.0212 0.0231 0.0217 0.0219 0.0211 0.0228 0.0208 0.0219 0.0203 0.0203 0.0208 0.0207 0.0205 0.0218 0.0207 0.0209 0.0202 0.0209 0.0201 0.0209 0.0197 0.0198 0.0202 0.0201 0.0201 0.0207 0.0200 0.0201 0.0197 0.0198 0.0196 0.0200 0.0194 0.0194 0.0199 0.0199 0.0199 0.0199 0.0196 0.0196 0.0195 0.0195 0.0195 0.0195 0.0194 0.0194 0.0201 0.0201 0.0200 0.0196 0.0198 0.0194 0.0197 0.0199 0.0197 0.0194 0.0195 0.0195 0.0208 0.0207 0.0203 0.0200 0.0204 0.0198 0.0203 0.0209 0.0202 0.0197 0.0198 0.0199 0.0219 0.0216 0.0209 0.0215 0.0215 0.0212 0.0213 0.0226 0.0210 0.0208 0.0203 0.0204 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters 0.9073 -22.5660 -3.9283 -3.5645 -25.0050 -17.0254 -1.3918 0.2995 1.8155 39.3132 -1.4267 -33.2832 eta,q 0.98065 13.75283 0.0210 0.0207 0.0202 0.0214 0.0209 0.0211 0.0207 0.0219 0.0205 0.0210 0.0201 0.0201 0.0201 0.0200 0.0197 0.0205 0.0201 0.0204 0.0200 0.0204 0.0199 0.0202 0.0197 0.0197 0.0195 0.0195 0.0194 0.0197 0.0196 0.0198 0.0195 0.0196 0.0195 0.0196 0.0194 0.0194 0.0194 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0195 0.0195 0.0195 0.0195 0.0195 0.0193 0.0195 0.0197 0.0195 0.0194 0.0195 0.0195 0.0201 0.0200 0.0199 0.0204 0.0201 0.0200 0.0199 0.0205 0.0199 0.0199 0.0197 0.0198 0.0211 0.0208 0.0204 0.0222 0.0211 0.0215 0.0206 0.0219 0.0205 0.0210 0.0201 0.0202 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters 0.9159 -22.5675 -3.9465 -3.4678 -25.0304 -16.8787 -1.4087 0.2984 1.8080 39.3963 -1.4711 -33.3610 eta,q 0.98069 13.75781 0.0206 0.0204 0.0200 0.0211 0.0205 0.0208 0.0203 0.0213 0.0202 0.0206 0.0199 0.0199 0.0199 0.0198 0.0197 0.0203 0.0199 0.0202 0.0197 0.0201 0.0197 0.0199 0.0195 0.0196 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0194 0.0195 0.0194 0.0195 0.0193 0.0194 0.0194 0.0194 0.0194 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0194 0.0194 0.0193 0.0194 0.0196 0.0194 0.0194 0.0194 0.0194 0.0199 0.0198 0.0197 0.0199 0.0199 0.0197 0.0197 0.0202 0.0197 0.0198 0.0196 0.0196 0.0206 0.0204 0.0201 0.0211 0.0206 0.0208 0.0203 0.0212 0.0202 0.0205 0.0199 0.0199 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters 0.9150 -22.5674 -3.9416 -3.3844 -25.0418 -16.7345 -1.4084 0.2865 1.7995 39.4387 -1.4814 -33.4056 eta,q 0.98072 13.76088 0.0202 0.0200 0.0198 0.0206 0.0201 0.0204 0.0200 0.0207 0.0199 0.0202 0.0197 0.0197 0.0197 0.0196 0.0195 0.0200 0.0197 0.0199 0.0196 0.0199 0.0195 0.0197 0.0194 0.0195 0.0194 0.0194 0.0194 0.0195 0.0194 0.0195 0.0194 0.0194 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0194 0.0194 0.0193 0.0193 0.0195 0.0193 0.0193 0.0193 0.0193 0.0197 0.0196 0.0195 0.0198 0.0197 0.0196 0.0196 0.0199 0.0196 0.0196 0.0195 0.0195 0.0202 0.0200 0.0198 0.0206 0.0202 0.0203 0.0200 0.0206 0.0199 0.0202 0.0197 0.0197 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters 0.9166 -22.5672 -3.9328 -3.3195 -25.0449 -16.5993 -1.4046 0.2706 1.7951 39.4725 -1.5194 -33.4297 eta,q 0.98075 13.76301 0.0198 0.0197 0.0196 0.0201 0.0198 0.0200 0.0197 0.0202 0.0196 0.0198 0.0195 0.0195 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0195 0.0196 0.0194 0.0195 0.0194 0.0194 0.0193 0.0193 0.0193 0.0194 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0196 0.0195 0.0195 0.0194 0.0197 0.0194 0.0195 0.0194 0.0194 0.0198 0.0197 0.0196 0.0201 0.0199 0.0200 0.0197 0.0202 0.0197 0.0198 0.0195 0.0195 registration optimization eta report parameter search radius 0.8000 0.8000 0.8000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 100000*second partial in parameter space 89. 74. 53. 14. 10. 12. 8. 16. 7. 10. 4. 5. 0.0198 0.0197 0.0196 0.0201 0.0198 0.0200 0.0197 0.0202 0.0196 0.0198 0.0195 0.0195 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0195 0.0196 0.0194 0.0195 0.0194 0.0194 0.0193 0.0193 0.0193 0.0194 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0196 0.0195 0.0195 0.0194 0.0197 0.0194 0.0195 0.0194 0.0194 0.0198 0.0197 0.0196 0.0201 0.0199 0.0200 0.0197 0.0202 0.0197 0.0198 0.0195 0.0195 0.9166 -22.5672 -3.9328 -3.3195 -25.0449 -16.5993 -1.4046 0.2706 1.7951 39.4725 -1.5194 -33.4297 eta,q 0.98075 13.76301 --------------------------------------------------------------------- imgreg_4dfp /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 2311 --------------------------------------------------------------------- $Id: imgreg_4dfp.c,v 1.3 2007/08/04 04:19:24 nicks Exp $ /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading mask: /pkg/brainmap/freesurfer-v4.0.1/average/711-2B_as_mni_average_305_mask.4dfp.img (2306576 pixels) talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 $Id: fimgreg.f,v 1.1 2007/05/04 22:33:59 nicks Exp $ image alignment mode 2311 decimal 907 hex parameters 0.9166 -22.5672 -3.9328 -3.3195 -25.0449 -16.5993 -1.4046 0.2706 1.7951 39.4725 -1.5194 -33.4297 eta,q 0.98075 13.76302 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters 0.8917 -22.5688 -3.9373 -3.8087 -25.1889 -17.1427 -1.3842 0.3075 1.8424 39.3550 -1.4436 -33.3779 eta,q 0.98057 13.74472 0.0215 0.0211 0.0206 0.0217 0.0212 0.0213 0.0211 0.0227 0.0209 0.0213 0.0204 0.0205 0.0203 0.0201 0.0199 0.0205 0.0203 0.0204 0.0202 0.0208 0.0201 0.0204 0.0198 0.0199 0.0195 0.0195 0.0194 0.0197 0.0196 0.0197 0.0196 0.0197 0.0196 0.0197 0.0195 0.0195 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0195 0.0195 0.0194 0.0196 0.0195 0.0195 0.0196 0.0198 0.0196 0.0196 0.0195 0.0196 0.0203 0.0201 0.0199 0.0210 0.0203 0.0208 0.0201 0.0208 0.0201 0.0203 0.0198 0.0199 0.0216 0.0211 0.0206 0.0235 0.0216 0.0232 0.0211 0.0225 0.0208 0.0217 0.0203 0.0204 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters 0.9209 -22.5560 -3.9580 -3.5596 -25.0760 -17.0411 -1.4115 0.3112 1.8233 39.3839 -1.4524 -33.3645 eta,q 0.98065 13.75388 0.0211 0.0208 0.0203 0.0218 0.0210 0.0212 0.0206 0.0219 0.0205 0.0209 0.0201 0.0202 0.0202 0.0201 0.0198 0.0207 0.0202 0.0204 0.0199 0.0204 0.0199 0.0202 0.0197 0.0197 0.0196 0.0196 0.0195 0.0199 0.0197 0.0198 0.0195 0.0196 0.0195 0.0196 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0194 0.0196 0.0196 0.0195 0.0194 0.0195 0.0193 0.0195 0.0197 0.0195 0.0194 0.0195 0.0195 0.0201 0.0200 0.0199 0.0201 0.0200 0.0199 0.0199 0.0205 0.0199 0.0200 0.0197 0.0197 0.0210 0.0208 0.0204 0.0216 0.0210 0.0214 0.0207 0.0219 0.0205 0.0210 0.0201 0.0201 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters 0.9164 -22.5624 -3.9538 -3.4683 -25.0505 -16.8878 -1.4113 0.2991 1.8071 39.4189 -1.4746 -33.3862 eta,q 0.98069 13.75802 0.0206 0.0204 0.0201 0.0211 0.0205 0.0208 0.0203 0.0212 0.0202 0.0205 0.0199 0.0199 0.0199 0.0198 0.0197 0.0203 0.0199 0.0202 0.0197 0.0201 0.0197 0.0199 0.0195 0.0196 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0194 0.0195 0.0194 0.0195 0.0194 0.0194 0.0194 0.0193 0.0194 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0194 0.0194 0.0193 0.0194 0.0196 0.0194 0.0194 0.0194 0.0194 0.0199 0.0198 0.0197 0.0200 0.0199 0.0197 0.0197 0.0202 0.0197 0.0198 0.0196 0.0196 0.0206 0.0204 0.0201 0.0211 0.0206 0.0208 0.0203 0.0212 0.0202 0.0206 0.0199 0.0199 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters 0.9167 -22.5655 -3.9455 -3.3824 -25.0481 -16.7397 -1.4099 0.2888 1.8021 39.4476 -1.4912 -33.4131 eta,q 0.98073 13.76097 0.0202 0.0200 0.0198 0.0206 0.0201 0.0204 0.0200 0.0207 0.0199 0.0202 0.0197 0.0197 0.0197 0.0196 0.0195 0.0200 0.0197 0.0199 0.0196 0.0199 0.0195 0.0197 0.0194 0.0195 0.0194 0.0194 0.0194 0.0195 0.0194 0.0195 0.0194 0.0194 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0194 0.0194 0.0193 0.0193 0.0195 0.0193 0.0193 0.0193 0.0193 0.0197 0.0196 0.0195 0.0198 0.0197 0.0196 0.0196 0.0199 0.0195 0.0196 0.0195 0.0195 0.0202 0.0200 0.0198 0.0206 0.0202 0.0203 0.0200 0.0206 0.0199 0.0202 0.0197 0.0197 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters 0.9175 -22.5662 -3.9332 -3.3191 -25.0492 -16.6012 -1.4133 0.2731 1.8001 39.4732 -1.5271 -33.4377 eta,q 0.98074 13.76308 0.0199 0.0197 0.0196 0.0201 0.0198 0.0200 0.0197 0.0202 0.0196 0.0198 0.0195 0.0195 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0194 0.0196 0.0194 0.0195 0.0194 0.0194 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0196 0.0195 0.0195 0.0194 0.0197 0.0194 0.0195 0.0194 0.0194 0.0198 0.0198 0.0196 0.0201 0.0199 0.0200 0.0197 0.0202 0.0197 0.0198 0.0195 0.0195 registration optimization eta report parameter search radius 0.8000 0.8000 0.8000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 2.4000 100000*second partial in parameter space 89. 74. 52. 14. 10. 12. 8. 16. 7. 10. 4. 5. 0.0199 0.0197 0.0196 0.0201 0.0198 0.0200 0.0197 0.0202 0.0196 0.0198 0.0195 0.0195 0.0195 0.0195 0.0194 0.0197 0.0195 0.0197 0.0194 0.0196 0.0194 0.0195 0.0194 0.0194 0.0193 0.0193 0.0193 0.0194 0.0194 0.0194 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0193 0.0194 0.0193 0.0193 0.0193 0.0193 0.0195 0.0195 0.0194 0.0196 0.0195 0.0195 0.0194 0.0197 0.0194 0.0195 0.0194 0.0194 0.0198 0.0198 0.0196 0.0201 0.0199 0.0200 0.0197 0.0202 0.0197 0.0198 0.0195 0.0195 0.9175 -22.5662 -3.9332 -3.3191 -25.0492 -16.6012 -1.4133 0.2731 1.8001 39.4732 -1.5271 -33.4377 eta,q 0.98074 13.76308 --------------------------------------------------------------------- compute_vox2vox talsrcimg talsrcimg_to_711-2C_as_mni_average_305_t4 /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305 --------------------------------------------------------------------- $Id: compute_vox2vox.c,v 1.2 2007/05/05 00:00:06 nicks Exp $ Reading: talsrcimg.4dfp.ifh Reading: talsrcimg_to_711-2C_as_mni_average_305_t4 Reading: /pkg/brainmap/freesurfer-v4.0.1/average/711-2C_as_mni_average_305.4dfp.ifh Writing: talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt start time Mon Oct 15 17:29:25 CDT 2007 end time Mon Oct 15 17:30:50 CDT 2007 mpr2mni305 success -------------------------------------------- tkregister2_cmdl --mov nu.mgz --targ /pkg/brainmap/freesurfer-v4.0.1/average/mni305.cor.mgz --xfmout transforms/talairach.auto.xfm --vox2vox talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt --noedit --reg talsrcimg.reg.tmp.dat Vox2Vox Matrix 0.967 -0.014 -0.003 5.487; 0.018 0.750 -0.395 102.456; 0.015 0.334 0.834 -27.605; 0.000 0.000 0.000 1.000; Can't find the talairach xform '/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm' Transform is not loaded into mri target volume /pkg/brainmap/freesurfer-v4.0.1/average/mni305.cor.mgz movable volume nu.mgz reg file talsrcimg.reg.tmp.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ Diagnostic Level -1 INFO: loading target /pkg/brainmap/freesurfer-v4.0.1/average/mni305.cor.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; Can't find the talairach xform '/disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/transforms/talairach.xfm' Transform is not loaded into mri INFO: loading movable nu.mgz Tmov: -------------------- -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; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.967 0.003 -0.014 0.920; -0.015 0.834 -0.334 -4.099; 0.018 0.395 0.750 -22.171; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.967 0.003 -0.014 0.920; -0.015 0.834 -0.334 -4.099; 0.018 0.395 0.750 -22.171; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 0.967 0.003 -0.014 0.920; -0.015 0.834 -0.334 -4.099; 0.018 0.395 0.750 -22.171; 0.000 0.000 0.000 1.000; register: file talsrcimg.reg.tmp.dat written `talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' -> `transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt' removed `talsrcimg.4dfp.hdr' removed `talsrcimg.4dfp.ifh' removed `talsrcimg.4dfp.img' removed `talsrcimg.4dfp.img.rec' removed `talsrcimg.hdr' removed `talsrcimg.img' removed `talsrcimg.mat' removed `talsrcimg.reg.tmp.dat' removed `talsrcimg_g11.4dfp.hdr' removed `talsrcimg_g11.4dfp.ifh' removed `talsrcimg_g11.4dfp.img' removed `talsrcimg_g11.4dfp.img.rec' removed `talsrcimg_to_711-2C_as_mni_average_305_t4' -------------------------------------------- Mon Oct 15 17:30:53 CDT 2007 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 15 17:30:54 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5178, pval=0.1531 >= threshold=0.0050) #-------------------------------------------- #@# Intensity Normalization Mon Oct 15 17:30:54 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.034 -0.010 0.015 -0.665; 0.007 0.990 0.442 13.846; -0.029 -0.521 1.101 22.305; 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 4 minutes and 37 seconds. white matter peak found at 111 gm peak at 72 (72), valley at 57 (57) csf peak at 21, setting threshold to 55 white matter peak found at 111 gm peak at 71 (71), valley at 45 (45) csf peak at 21, setting threshold to 54 #-------------------------------------------- #@# Skull Stripping Mon Oct 15 17:35:33 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_em_register -skull nu.mgz /pkg/brainmap/freesurfer-v4.0.1/average/RB_all_withskull_2007-08-08.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 '/pkg/brainmap/freesurfer-v4.0.1/average/RB_all_withskull_2007-08-08.gca'... average std = 22.7 using min determinant for regularization = 51.6 0 singular and 4896 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.1 or > 846.9 total sample mean = 92.0 (1434 zeros) ************************************************ spacing=8, using 3350 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3350, passno 0, spacing 8 resetting wm mean[0]: 117 --> 127 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=15.0 using (100, 85, 127) as brain centroid... mean wm in atlas = 127, using box (80,53,99) --> (119, 116,154) to find MRI wm before smoothing, mri peak at 20 after smoothing, mri peak at 20, scaling input intensities by 6.350 scaling channel 0 by 6.35 initial log_p = -24690.0 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-52.8, 35.8, -47.2): log p = -73224.3 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-52278.4, old_max_log_p =-73224.3 (thresh=-73151.1) 1.081 -0.510 0.025 -37.106; 0.485 1.044 0.323 -97.490; -0.160 -0.282 1.150 -40.669; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-27737.8, old_max_log_p =-52278.4 (thresh=-52226.1) 1.018 -0.664 -0.750 128.300; 0.941 0.702 0.656 -214.305; 0.067 -1.022 0.996 -24.918; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-21922.9, old_max_log_p =-27737.8 (thresh=-27710.1) 1.494 -0.331 -0.433 -15.885; 0.469 0.522 1.482 -300.752; -0.123 -1.559 0.655 96.550; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-19192.2, old_max_log_p =-21922.9 (thresh=-21901.0) 1.874 0.033 -0.110 -179.540; 0.055 0.563 1.900 -342.985; 0.091 -1.923 0.631 96.981; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-17639.1, old_max_log_p =-19192.2 (thresh=-19173.0) 2.205 0.323 -0.223 -244.016; 0.066 0.673 2.271 -457.196; 0.408 -2.018 0.646 68.836; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-17021.0, old_max_log_p =-17639.1 (thresh=-17621.5) 2.474 -0.028 -0.562 -180.892; 0.517 0.461 2.739 -636.263; 0.100 -2.530 0.420 229.636; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16363.1, old_max_log_p =-17021.0 (thresh=-17004.0) 2.985 0.368 -0.198 -403.848; 0.213 0.122 3.364 -704.088; 0.405 -2.557 -0.101 303.847; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16352.0, old_max_log_p =-16363.1 (thresh=-16346.8) 2.977 0.431 0.270 -523.823; -0.279 0.447 3.549 -696.631; 0.458 -2.673 0.391 199.501; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 8 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16164.7, old_max_log_p =-16352.0 (thresh=-16335.6) 3.140 0.349 0.157 -521.061; -0.119 0.175 3.522 -690.543; 0.371 -2.676 0.008 304.697; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 9 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16035.0, old_max_log_p =-16164.7 (thresh=-16148.5) 3.077 0.430 0.049 -492.786; 0.022 0.011 3.685 -737.859; 0.510 -2.750 -0.230 336.349; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 10 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16035.0, old_max_log_p =-16035.0 (thresh=-16018.9) 3.077 0.430 0.049 -492.786; 0.022 0.011 3.685 -737.859; 0.510 -2.750 -0.230 336.349; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 11 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-15938.1, old_max_log_p =-16035.0 (thresh=-16018.9) 3.085 0.455 0.051 -497.687; 0.026 -0.013 3.640 -726.253; 0.535 -2.736 -0.261 337.415; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 12 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-15938.1, old_max_log_p =-15938.1 (thresh=-15922.2) 3.085 0.455 0.051 -497.687; 0.026 -0.013 3.640 -726.253; 0.535 -2.736 -0.261 337.415; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3350 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 3.08478 0.45532 0.05119 -497.68695; 0.02630 -0.01298 3.63982 -726.25323; 0.53489 -2.73555 -0.26073 337.41528; 0.00000 0.00000 0.00000 1.00000; nsamples 3350 Quasinewton: input matrix 3.08478 0.45532 0.05119 -497.68695; 0.02630 -0.01298 3.63982 -726.25323; 0.53489 -2.73555 -0.26073 337.41528; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 pass 2 through quasi-newton minimization... v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 013: -log(p) = 15938.1 tol 0.000010 Resulting transform: 3.085 0.455 0.051 -497.687; 0.026 -0.013 3.640 -726.253; 0.535 -2.736 -0.261 337.415; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -15938.1 (old=-24690.0) transform before final EM align: 3.085 0.455 0.051 -497.687; 0.026 -0.013 3.640 -726.253; 0.535 -2.736 -0.261 337.415; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 380045 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 3.08478 0.45532 0.05119 -497.68695; 0.02630 -0.01298 3.63982 -726.25323; 0.53489 -2.73555 -0.26073 337.41528; 0.00000 0.00000 0.00000 1.00000; nsamples 380045 Quasinewton: input matrix 3.08478 0.45532 0.05119 -497.68695; 0.02630 -0.01298 3.63982 -726.25323; 0.53489 -2.73555 -0.26073 337.41528; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 pass 2 through quasi-newton minimization... v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 013: -log(p) = 307135456.0 tol 0.000000 final transform: 3.085 0.455 0.051 -497.687; 0.026 -0.013 3.640 -726.253; 0.535 -2.736 -0.261 337.415; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 46 minutes and 28 seconds. mri_watershed -brain_atlas /pkg/brainmap/freesurfer-v4.0.1/average/RB_all_withskull_2007-08-08.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=176 y=91 z=226 r=35 first estimation of the main basin volume: 193282 voxels mean intensity too low ! Modification of the image: intensity*8.89 first estimation of the COG coord: x=176 y=91 z=226 r=35 first estimation of the main basin volume: 193282 voxels Looking for seedpoints 2 found in the cerebellum 0 found in the rest of the brain global maximum in x=161, y=67, z=235, Imax=255 CSF=21, WM_intensity=145, WM_VARIANCE=10 WM_MIN=127, WM_HALF_MIN=142, WM_HALF_MAX=151, WM_MAX=157 preflooding height equal to 10 percent done Analyze main basin size=891787749 voxels, voxel volume =1.000 = 891787749 mmm3 = 891787.749 cm3 done PostAnalyze...Basin Prior 228 basins merged thanks to atlas ambiguous basin, merged: at least 3 ambiguous voxels; size: 23 voxels ambiguous basin, merged: at least 6 ambiguous voxels; size: 140 voxels ambiguous basin, merged: at least 5 ambiguous voxels; size: 92 voxels ambiguous basin, merged: at least 11 ambiguous voxels; size: 1116 voxels ambiguous basin, merged: at least 6 ambiguous voxels; size: 169 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 14 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 15 voxels ambiguous basin, merged: at least 13 ambiguous voxels; size: 1831 voxels ambiguous basin, merged: at least 20 ambiguous voxels; size: 7983 voxels ambiguous basin, merged: at least 29 ambiguous voxels; size: 22015 voxels ambiguous basin, merged: at least 4 ambiguous voxels; size: 37 voxels ambiguous basin, merged: at least 12 ambiguous voxels; size: 1700 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 21 voxels ambiguous basin, merged: at least 15 ambiguous voxels; size: 3236 voxels ambiguous basin, merged: at least 6 ambiguous voxels; size: 173 voxels ambiguous basin, merged: at least 27 ambiguous voxels; size: 17694 voxels ambiguous basin, merged: at least 9 ambiguous voxels; size: 607 voxels ambiguous basin, merged: at least 12 ambiguous voxels; size: 1554 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels ambiguous basin, merged: at least 14 ambiguous voxels; size: 2379 voxels ambiguous basin, merged: at least 8 ambiguous voxels; size: 391 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 11 voxels ambiguous basin, merged: at least 14 ambiguous voxels; size: 2676 voxels ambiguous basin, merged: at least 14 ambiguous voxels; size: 2446 voxels ambiguous basin, merged: at least 6 ambiguous voxels; size: 162 voxels ambiguous basin, merged: at least 4 ambiguous voxels; size: 30 voxels ambiguous basin, merged: at least 12 ambiguous voxels; size: 1525 voxels ambiguous basin, merged: at least 25 ambiguous voxels; size: 14602 voxels ambiguous basin, merged: at least 11 ambiguous voxels; size: 1113 voxels ambiguous basin, merged: at least 3 ambiguous voxels; size: 19 voxels ***** 31 basin(s) merged in 4 iteration(s) ***** 83799 voxel(s) added to the main basin ambiguous basin, non merged: 3 ambiguous voxels; size: 27183 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels ambiguous basin, non merged: 9 ambiguous voxels; size: 1369 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 1 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels ambiguous basin, non merged: 8 ambiguous voxels; size: 2590 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 4 voxels ambiguous basin, non merged: 0 ambiguous voxels; size: 3 voxels ambiguous basin, non merged: 19 ambiguous voxels; size: 16870 voxels ambiguous basin, non merged: 3 ambiguous voxels; size: 1300 voxels done Weighting the input with before template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=181,y=98, z=230, r=4548 iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 6474 RIGHT_CER CSF_MIN=48, CSF_intensity=49, CSF_MAX=55 , nb = 412 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 137291790 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 321 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 3091 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=3 , nb = 740 Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 3, 10, 65, 72 after analyzing : 3, 46, 65, 52 RIGHT_CER before analyzing : 55, 53, 45, 72 after analyzing : 51, 53, 53, 57 LEFT_CER before analyzing : 3, 4, 36, 60 after analyzing : 3, 25, 36, 33 RIGHT_BRAIN before analyzing : 3, 9, 65, 74 after analyzing : 3, 46, 65, 53 LEFT_BRAIN before analyzing : 3, 5, 43, 60 after analyzing : 3, 30, 43, 37 OTHER before analyzing : 3, 8, 64, 74 after analyzing : 3, 45, 64, 52 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.025, std = 0.028 curvature mean = 33.669, std = 4.238 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 33.90, sigma = 106.60 after rotation: sse = 33.90, sigma = 106.60 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 47.06, its var is 82.32 before Erosion-Dilatation 41.91% of inacurate vertices after Erosion-Dilatation 60.16% of inacurate vertices 54.82% of 'positive' inacurate vertices 45.18% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 159357 voxels, voxel volume = 1.000 mm3 = 159357 mmm3 = 159.357 cm3 ****************************** Save...done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ recon-all finished without error at Mon Oct 15 18:24:26 CDT 2007 New invocation of recon-all Mon Oct 15 21:51:51 EDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 /pkg/brainmap/freesurfer-v3.0.5/bin//recon-all -autorecon2 -subjid 990903_61167 subjid 990903_61167 setenv SUBJECTS_DIR /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 Actual FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 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 32 kbytes maxproc 40960 ######################################## program versions used $Id: recon-all,v 1.17.2.16 2006/12/12 19:44:21 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_fix_topology.c,v 1.41.2.1 2007/01/05 16:58:33 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-01:51:52-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: mharms Machine: eli Platform: Linux PlatformVersion: 2.6.9-34.0.1.ELsmp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /pkg/brainmap/freesurfer-v3.0.5 Previous: /pkg/brainmap/freesurfer-v4.0.1 #------------------------------------- #@# EM Registration Mon Oct 15 21:51:53 EDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_em_register -mask brainmask.mgz nu.mgz /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... mghRead: encountered error executing: 'zcat /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/nu.mgz',frame -1 mri_em_register: could not open input volume nu.mgz. Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Oct 15 21:51:57 EDT 2007 New invocation of recon-all Tue Oct 16 15:00:29 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 /pkg/brainmap/freesurfer-v3.0.5/bin//recon-all -autorecon2 -subjid 990903_61167 subjid 990903_61167 setenv SUBJECTS_DIR /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 Actual FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v3.0.5 Linux vader 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 78848 ######################################## program versions used $Id: recon-all,v 1.17.2.16 2006/12/12 19:44:21 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:29-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_fix_topology.c,v 1.41.2.1 2007/01/05 16:58:33 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:00:30-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /pkg/brainmap/freesurfer-v3.0.5 Previous: /pkg/brainmap/freesurfer-v4.0.1 New invocation of recon-all Tue Oct 16 15:01:20 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 /pkg/brainmap/freesurfer-v3.0.5/bin//recon-all -autorecon2 -subjid 990903_61167 subjid 990903_61167 setenv SUBJECTS_DIR /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 Actual FREESURFER_HOME /pkg/brainmap/freesurfer-v3.0.5 build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v3.0.5 Linux vader 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 78848 ######################################## program versions used $Id: recon-all,v 1.17.2.16 2006/12/12 19:44:21 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version stable3 # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_fix_topology.c,v 1.41.2.1 2007/01/05 16:58:33 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable3 $ TimeStamp: 07/10/16-20:01:21-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: mharms Machine: vader Platform: Linux PlatformVersion: 2.6.9-5.ELsmp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /pkg/brainmap/freesurfer-v3.0.5 Previous: /pkg/brainmap/freesurfer-v4.0.1 #------------------------------------- #@# EM Registration Tue Oct 16 15:01:22 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_em_register -mask brainmask.mgz nu.mgz /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-58.5, 13.1, -58.5): log p = -187912.6 Result so far: scale 1.000: max_log_p=-183122.2, old_max_log_p =-187912.6 (thresh=-187724.7) 1.088 0.459 -0.166 -88.612; -0.482 1.084 -0.126 121.608; 0.115 0.204 1.042 -108.117; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-171523.0, old_max_log_p =-183122.2 (thresh=-182939.0) 1.189 0.773 0.155 -198.373; -0.668 1.110 -0.321 179.873; -0.351 0.233 1.214 -77.861; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-131033.8, old_max_log_p =-171523.0 (thresh=-171351.5) 0.826 1.458 0.174 -198.658; -1.082 0.662 -0.919 432.241; -0.991 0.354 1.188 13.614; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-77831.4, old_max_log_p =-131033.8 (thresh=-130902.8) 0.151 1.907 0.462 -198.799; -1.178 0.393 -1.377 584.576; -1.625 -0.228 1.076 199.340; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-45429.4, old_max_log_p =-77831.4 (thresh=-77753.5) -0.346 2.298 0.143 -74.149; -1.142 -0.139 -1.885 757.117; -2.089 -0.438 1.045 303.264; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-34715.7, old_max_log_p =-45429.4 (thresh=-45383.9) -0.569 2.636 -0.527 64.243; -0.094 -0.688 -2.517 767.644; -2.817 -0.651 0.232 639.794; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-31905.2, old_max_log_p =-34715.7 (thresh=-34681.0) -1.801 2.122 -1.196 501.018; 0.328 -1.566 -2.746 835.579; -2.323 -1.664 0.540 589.949; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-31471.0, old_max_log_p =-31905.2 (thresh=-31873.3) -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-31471.0, old_max_log_p =-31471.0 (thresh=-31439.5) -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix -2.04101 1.63345 -1.48040 652.89258; 0.65621 -1.92447 -2.72526 808.18542; -1.92126 -1.82154 0.65718 506.37585; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix -2.04101 1.63345 -1.48040 652.89258; 0.65621 -1.92447 -2.72526 808.18542; -1.92126 -1.82154 0.65718 506.37585; 0.00000 0.00000 0.00000 1.00000; fp = 31471.001953, fret = 31471.001953, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix -2.04101 1.63345 -1.48040 652.89258; 0.65621 -1.92447 -2.72526 808.18542; -1.92126 -1.82154 0.65718 506.37585; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix -2.04101 1.63345 -1.48040 652.89258; 0.65621 -1.92447 -2.72526 808.18542; -1.92126 -1.82154 0.65718 506.37585; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... fp = 3063329.750000, fret = 3063329.750000, ftol = 0.000000, EPS = 0.000000 freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=6.5 using (173, 95, 227) as brain centroid... mean wm in atlas = 116, using box (167,88,220) --> (179, 102,233) to find MRI wm before smoothing, mri peak at 17 after smoothing, mri peak at 18, scaling input intensities by 6.444 scaling channel 0 by 6.44444 initial log_p = -217165.3 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** **************************************** Nine parameter search. iteration 3 nscales = 3 ... **************************************** **************************************** Nine parameter search. iteration 4 nscales = 4 ... **************************************** **************************************** Nine parameter search. iteration 5 nscales = 5 ... **************************************** **************************************** Nine parameter search. iteration 6 nscales = 6 ... **************************************** **************************************** Nine parameter search. iteration 7 nscales = 7 ... **************************************** **************************************** Nine parameter search. iteration 8 nscales = 8 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 009: -log(p) = 31471.0 after pass:transform: ( -2.04, 1.63, -1.48, 652.89) ( 0.66, -1.92, -2.73, 808.19) ( -1.92, -1.82, 0.66, 506.38) outof QuasiNewtonEMA: 011: -log(p) = 31471.0 tol 0.000010 Resulting transform: -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -31471.0 (old=-217165.3) transform before final EM align: -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 010: -log(p) = 3063384.5 after pass:transform: ( -2.04, 1.63, -1.48, 652.89) ( 0.66, -1.92, -2.73, 808.19) ( -1.92, -1.82, 0.66, 506.38) dfp_em_step_func: 011: -log(p) = 3063337.0 after pass:transform: ( -2.04, 1.63, -1.48, 652.89) ( 0.66, -1.92, -2.73, 808.19) ( -1.92, -1.82, 0.66, 506.38) dfp_em_step_func: 012: -log(p) = 3063329.8 after pass:transform: ( -2.04, 1.63, -1.48, 652.89) ( 0.66, -1.92, -2.73, 808.19) ( -1.92, -1.82, 0.66, 506.38) outof QuasiNewtonEMA: 014: -log(p) = 3063329.8 tol 0.000000 final transform: -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 22 minutes and 44 seconds. #-------------------------------------- #@# CA Normalize Tue Oct 16 15:24:06 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=6.5 using (173, 95, 227) as brain centroid... mean wm in atlas = 116, using box (167,88,220) --> (179, 102,233) to find MRI wm before smoothing, mri peak at 17 after smoothing, mri peak at 18, scaling input intensities by 6.444 scaling channel 0 by 6.44444 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (156, 85, 202) --> (204, 131, 237) Left_Cerebral_White_Matter: limiting intensities to 112.0 --> 117.0 137 of 159 (86.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (162, 80, 211) --> (210, 124, 243) Right_Cerebral_White_Matter: limiting intensities to 111.0 --> 117.0 122 of 136 (89.7%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (182, 102, 196) --> (198, 119, 213) Left_Cerebellum_White_Matter: limiting intensities to 97.0 --> 104.0 2 of 9 (22.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (189, 97, 205) --> (208, 113, 215) Right_Cerebellum_White_Matter: limiting intensities to 103.0 --> 110.0 0 of 6 (0.0%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (181, 97, 199) --> (195, 109, 220) Brain_Stem: limiting intensities to 111.0 --> 117.0 24 of 30 (80.0%) samples deleted using 340 total control points for intensity normalization... bias field = 0.951 +- 0.080 0 of 27 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 53 seconds. #-------------------------------------- #@# CA Reg Tue Oct 16 15:25:59 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca transforms/talairach.m3z renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 not handling expanded ventricles... using MR volume brainmask.mgz to mask input volume... using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) renormalizing by structure alignment.... renormalizing input #0 aligning Left_Pallidum... invalid transform detected (det=6.7681) gca peak = 0.11705 (100) uniform distribution in MR - rejecting arbitrary fit aligning Right_Pallidum... gca peak = 0.13501 (106) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_White_Matter... invalid transform detected (det=0.1495) gca peak = 0.05652 (116) mri peak = 0.10828 (111) Right_Cerebral_White_Matter (41): linear fit = 0.95 x + 0.0 (279 voxels, overlap=0.362) aligning Left_Cerebral_White_Matter... gca peak = 0.05682 (116) mri peak = 0.29161 (105) Left_Cerebral_White_Matter (2): linear fit = 0.93 x + 0.0 (487 voxels, overlap=0.182) aligning Left_Lateral_Ventricle... gca peak = 0.05153 (25) uniform distribution in MR - rejecting arbitrary fit aligning Right_Lateral_Ventricle... gca peak = 0.07557 (30) uniform distribution in MR - rejecting arbitrary fit aligning Right_Hippocampus... gca peak = 0.14805 (66) uniform distribution in MR - rejecting arbitrary fit aligning Left_Hippocampus... gca peak = 0.17297 (66) uniform distribution in MR - rejecting arbitrary fit aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.13478 (105) aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.05511 (96) aligning Right_Caudate... gca peak = 0.07786 (81) mri peak = 0.20023 (122) aligning Left_Caudate... gca peak = 0.07814 (81) uniform distribution in MR - rejecting arbitrary fit aligning Left_Cerebellum_Cortex... gca peak = 0.06033 (63) mri peak = 0.15200 (102) overlap = 1.09491e-06, overlap_threshold = 0.001 insufficient overlap 0.0000 in histograms - rejecting aligning Right_Cerebellum_Cortex... gca peak = 0.05990 (64) mri peak = 0.17233 (101) overlap = 5.4717e-05, overlap_threshold = 0.001 insufficient overlap 0.0001 in histograms - rejecting aligning Left_Cerebellum_White_Matter... gca peak = 0.09299 (92) mri peak = 0.15614 (102) Left_Cerebellum_White_Matter (7): linear fit = 1.17 x + 0.0 (315 voxels, overlap=0.144) aligning Right_Cerebellum_White_Matter... gca peak = 0.08899 (93) mri peak = 0.17853 (101) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (191 voxels, overlap=0.251) aligning Left_Amygdala... gca peak = 0.13911 (71) uniform distribution in MR - rejecting arbitrary fit aligning Right_Amygdala... gca peak = 0.15703 (65) uniform distribution in MR - rejecting arbitrary fit aligning Left_Thalamus_Proper... gca peak = 0.06537 (100) mri peak = 0.10119 (104) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (80 voxels, overlap=0.348) aligning Right_Thalamus_Proper... gca peak = 0.07019 (99) mri peak = 0.17386 (110) Right_Thalamus_Proper (49): linear fit = 1.17 x + 0.0 (185 voxels, overlap=0.189) aligning Left_Putamen... gca peak = 0.09468 (90) uniform distribution in MR - rejecting arbitrary fit aligning Right_Putamen... gca peak = 0.07184 (82) mri peak = 0.16016 (110) aligning Brain_Stem... gca peak = 0.05597 (80) mri peak = 0.08788 (109) Brain_Stem (16): linear fit = 1.20 x + 0.0 (410 voxels, overlap=0.135) aligning Right_VentralDC... gca peak = 0.05879 (97) mri peak = 0.17038 (115) aligning Left_VentralDC... gca peak = 0.06932 (98) uniform distribution in MR - rejecting arbitrary fit aligning Third_Ventricle... gca peak = 0.10105 (38) uniform distribution in MR - rejecting arbitrary fit aligning Fourth_Ventricle... gca peak = 0.10426 (32) not using caudate to estimate GM means uniform distribution in MR - rejecting arbitrary fit estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 0.94 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 6 transforms computed rms increased - undoing step... 0000: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN rms increased - undoing step... 0002: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN rms increased - undoing step... 0004: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN rms increased - undoing step... 0006: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN rms increased - undoing step... 0008: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN rms increased - undoing step... 0010: dt=0.000000, rms=1.237 (-0.146%), neg=0, invalid=1511, LIN label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.229, neg=0, invalid=1511 0013: dt=78.008228, rms=1.171 (4.708%), neg=0, invalid=1511 0014: dt=32.368000, rms=1.145 (2.272%), neg=0, invalid=1511 0015: dt=32.368000, rms=1.126 (1.611%), neg=0, invalid=1511 0016: dt=27.744000, rms=1.113 (1.217%), neg=0, invalid=1511 0017: dt=8.092000, rms=1.110 (0.205%), neg=0, invalid=1511 0018: dt=8.092000, rms=1.109 (0.159%), neg=0, invalid=1511 0019: dt=32.368000, rms=1.103 (0.478%), neg=0, invalid=1511 0020: dt=23.120000, rms=1.095 (0.713%), neg=0, invalid=1511 0021: dt=23.120000, rms=1.087 (0.766%), neg=0, invalid=1511 0022: dt=0.000000, rms=1.087 (-0.002%), neg=0, invalid=1511 0023: dt=0.850000, rms=1.087 (-0.025%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.087, neg=0, invalid=1511 0024: dt=44.306907, rms=1.078 (0.805%), neg=0, invalid=1511 0025: dt=53.820423, rms=1.043 (3.285%), neg=0, invalid=1511 0026: dt=7.219879, rms=1.041 (0.206%), neg=0, invalid=1511 0027: dt=4.738563, rms=1.040 (0.030%), neg=0, invalid=1511 0028: dt=4.738563, rms=1.040 (0.005%), neg=0, invalid=1511 0029: dt=4.738563, rms=1.040 (-0.061%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.041, neg=0, invalid=1511 0030: dt=10.788281, rms=1.027 (1.310%), neg=0, invalid=1511 0031: dt=2.268000, rms=1.018 (0.858%), neg=0, invalid=1511 0032: dt=7.776000, rms=0.998 (2.053%), neg=0, invalid=1511 0033: dt=0.000000, rms=0.998 (-0.000%), neg=0, invalid=1511 0034: dt=0.450000, rms=0.998 (-0.141%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.998, neg=0, invalid=1511 0035: dt=0.000000, rms=0.998 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.000, neg=0, invalid=1511 0036: dt=0.031250, rms=1.000 (0.002%), neg=0, invalid=1511 0037: dt=0.200831, rms=1.000 (0.035%), neg=0, invalid=1511 0038: dt=0.700000, rms=0.993 (0.697%), neg=0, invalid=1511 0039: dt=0.175000, rms=0.991 (0.126%), neg=0, invalid=1511 0040: dt=0.700000, rms=0.983 (0.873%), neg=0, invalid=1511 0041: dt=0.700000, rms=0.976 (0.712%), neg=0, invalid=1511 0042: dt=0.500000, rms=0.971 (0.506%), neg=0, invalid=1511 0043: dt=0.175000, rms=0.969 (0.159%), neg=0, invalid=1511 0044: dt=0.700000, rms=0.962 (0.732%), neg=0, invalid=1511 0045: dt=0.175000, rms=0.961 (0.146%), neg=0, invalid=1511 0046: dt=0.700000, rms=0.955 (0.633%), neg=0, invalid=1511 0047: dt=0.175000, rms=0.953 (0.144%), neg=0, invalid=1511 0048: dt=0.700000, rms=0.948 (0.584%), neg=0, invalid=1511 0049: dt=0.175000, rms=0.946 (0.134%), neg=0, invalid=1511 0050: dt=0.700000, rms=0.941 (0.538%), neg=0, invalid=1511 0051: dt=0.700000, rms=0.937 (0.501%), neg=0, invalid=1511 0052: dt=0.500000, rms=0.933 (0.338%), neg=0, invalid=1511 0053: dt=0.175000, rms=0.932 (0.113%), neg=0, invalid=1511 0054: dt=0.700000, rms=0.928 (0.459%), neg=0, invalid=1511 0055: dt=0.175000, rms=0.927 (0.092%), neg=0, invalid=1511 0056: dt=0.700000, rms=0.923 (0.417%), neg=0, invalid=1511 0057: dt=0.175000, rms=0.923 (0.094%), neg=0, invalid=1511 0058: dt=0.500000, rms=0.920 (0.291%), neg=0, invalid=1511 0059: dt=0.175000, rms=0.919 (0.090%), neg=0, invalid=1511 0060: dt=0.037500, rms=0.919 (0.021%), neg=0, invalid=1511 0061: dt=0.002344, rms=0.919 (0.001%), neg=0, invalid=1511 0062: dt=0.000293, rms=0.919 (0.000%), neg=0, invalid=1511 0063: dt=0.000146, rms=0.919 (0.000%), neg=0, invalid=1511 0064: dt=0.000000, rms=0.919 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.919, neg=0, invalid=1511 0065: dt=2.400000, rms=0.910 (0.995%), neg=0, invalid=1511 0066: dt=0.700000, rms=0.907 (0.312%), neg=0, invalid=1511 0067: dt=0.600000, rms=0.904 (0.311%), neg=0, invalid=1511 0068: dt=0.175000, rms=0.904 (0.028%), neg=0, invalid=1511 0069: dt=0.175000, rms=0.903 (0.083%), neg=0, invalid=1511 0070: dt=0.175000, rms=0.902 (0.153%), neg=0, invalid=1511 0071: dt=0.175000, rms=0.900 (0.208%), neg=0, invalid=1511 0072: dt=0.175000, rms=0.898 (0.246%), neg=0, invalid=1511 0073: dt=0.175000, rms=0.895 (0.281%), neg=0, invalid=1511 0074: dt=0.175000, rms=0.892 (0.314%), neg=0, invalid=1511 0075: dt=0.175000, rms=0.889 (0.336%), neg=0, invalid=1511 0076: dt=0.175000, rms=0.886 (0.351%), neg=0, invalid=1511 0077: dt=0.175000, rms=0.883 (0.362%), neg=0, invalid=1511 0078: dt=0.175000, rms=0.883 (0.043%), neg=0, invalid=1511 0079: dt=0.175000, rms=0.882 (0.083%), neg=0, invalid=1511 0080: dt=0.175000, rms=0.881 (0.121%), neg=0, invalid=1511 0081: dt=0.175000, rms=0.879 (0.154%), neg=0, invalid=1511 0082: dt=0.175000, rms=0.878 (0.181%), neg=0, invalid=1511 0083: dt=0.175000, rms=0.876 (0.202%), neg=0, invalid=1511 0084: dt=0.175000, rms=0.874 (0.225%), neg=0, invalid=1511 0085: dt=0.175000, rms=0.872 (0.243%), neg=0, invalid=1511 0086: dt=0.175000, rms=0.870 (0.262%), neg=0, invalid=1511 0087: dt=0.175000, rms=0.867 (0.276%), neg=0, invalid=1511 0088: dt=0.175000, rms=0.865 (0.285%), neg=0, invalid=1511 0089: dt=0.175000, rms=0.862 (0.285%), neg=0, invalid=1511 0090: dt=0.175000, rms=0.860 (0.283%), neg=0, invalid=1511 0091: dt=0.175000, rms=0.857 (0.277%), neg=0, invalid=1511 0092: dt=0.043750, rms=0.857 (0.006%), neg=0, invalid=1511 0093: dt=0.005469, rms=0.857 (0.001%), neg=0, invalid=1511 0094: dt=0.001250, rms=0.857 (0.000%), neg=0, invalid=1511 0095: dt=0.000156, rms=0.857 (0.000%), neg=0, invalid=1511 0096: dt=0.000078, rms=0.857 (0.000%), neg=0, invalid=1511 0097: dt=0.000002, rms=0.857 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.870, neg=0, invalid=1511 0098: dt=0.180000, rms=0.869 (0.108%), neg=0, invalid=1511 0099: dt=0.063000, rms=0.868 (0.061%), neg=0, invalid=1511 0100: dt=0.063000, rms=0.868 (0.064%), neg=0, invalid=1511 0101: dt=0.063000, rms=0.867 (0.066%), neg=0, invalid=1511 0102: dt=0.063000, rms=0.867 (0.058%), neg=0, invalid=1511 0103: dt=0.054000, rms=0.866 (0.055%), neg=0, invalid=1511 0104: dt=0.063000, rms=0.866 (0.062%), neg=0, invalid=1511 0105: dt=0.054000, rms=0.865 (0.055%), neg=0, invalid=1511 0106: dt=0.063000, rms=0.865 (0.062%), neg=0, invalid=1511 0107: dt=0.063000, rms=0.864 (0.064%), neg=0, invalid=1511 0108: dt=0.063000, rms=0.864 (0.058%), neg=0, invalid=1511 0109: dt=0.063000, rms=0.863 (0.066%), neg=0, invalid=1511 0110: dt=0.063000, rms=0.863 (0.064%), neg=0, invalid=1511 0111: dt=0.063000, rms=0.862 (0.066%), neg=0, invalid=1511 0112: dt=0.063000, rms=0.861 (0.064%), neg=0, invalid=1511 0113: dt=0.063000, rms=0.861 (0.064%), neg=0, invalid=1511 0114: dt=0.063000, rms=0.860 (0.059%), neg=0, invalid=1511 0115: dt=0.063000, rms=0.860 (0.062%), neg=0, invalid=1511 0116: dt=0.063000, rms=0.859 (0.058%), neg=0, invalid=1511 0117: dt=0.054000, rms=0.859 (0.051%), neg=0, invalid=1511 0118: dt=0.063000, rms=0.858 (0.059%), neg=0, invalid=1511 0119: dt=0.063000, rms=0.858 (0.060%), neg=0, invalid=1511 0120: dt=0.063000, rms=0.857 (0.058%), neg=0, invalid=1511 0121: dt=0.054000, rms=0.857 (0.049%), neg=0, invalid=1511 0122: dt=0.054000, rms=0.857 (0.050%), neg=0, invalid=1511 0123: dt=0.054000, rms=0.856 (0.092%), neg=0, invalid=1511 0124: dt=0.054000, rms=0.855 (0.131%), neg=0, invalid=1511 0125: dt=0.054000, rms=0.853 (0.163%), neg=0, invalid=1511 0126: dt=0.054000, rms=0.852 (0.190%), neg=0, invalid=1511 0127: dt=0.054000, rms=0.850 (0.204%), neg=0, invalid=1511 0128: dt=0.054000, rms=0.848 (0.224%), neg=0, invalid=1511 0129: dt=0.054000, rms=0.846 (0.238%), neg=0, invalid=1511 0130: dt=0.054000, rms=0.844 (0.243%), neg=0, invalid=1511 0131: dt=0.054000, rms=0.844 (0.026%), neg=0, invalid=1511 0132: dt=0.054000, rms=0.843 (0.047%), neg=0, invalid=1511 0133: dt=0.054000, rms=0.843 (0.070%), neg=0, invalid=1511 0134: dt=0.054000, rms=0.842 (0.094%), neg=0, invalid=1511 0135: dt=0.054000, rms=0.841 (0.110%), neg=0, invalid=1511 0136: dt=0.054000, rms=0.841 (0.030%), neg=0, invalid=1511 0137: dt=0.054000, rms=0.840 (0.028%), neg=0, invalid=1511 0138: dt=0.013500, rms=0.840 (0.008%), neg=0, invalid=1511 0139: dt=0.006750, rms=0.840 (0.004%), neg=0, invalid=1511 0140: dt=0.000984, rms=0.840 (0.001%), neg=0, invalid=1511 0141: dt=0.000984, rms=0.840 (-0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.840, neg=0, invalid=1511 0142: dt=0.003938, rms=0.840 (0.002%), neg=0, invalid=1511 0143: dt=0.003375, rms=0.840 (0.002%), neg=0, invalid=1511 0144: dt=0.000211, rms=0.840 (0.000%), neg=0, invalid=1511 0145: dt=0.000105, rms=0.840 (0.000%), neg=0, invalid=1511 0146: dt=0.000026, rms=0.840 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.870, neg=0, invalid=1511 0147: dt=0.028000, rms=0.869 (0.008%), neg=0, invalid=1511 0148: dt=0.007000, rms=0.869 (0.003%), neg=0, invalid=1511 0149: dt=0.007000, rms=0.869 (0.003%), neg=0, invalid=1511 0150: dt=0.007000, rms=0.869 (0.005%), neg=0, invalid=1511 0151: dt=0.007000, rms=0.869 (0.007%), neg=0, invalid=1511 0152: dt=0.007000, rms=0.869 (0.008%), neg=0, invalid=1511 0153: dt=0.007000, rms=0.869 (0.013%), neg=0, invalid=1511 0154: dt=0.007000, rms=0.869 (0.014%), neg=0, invalid=1511 0155: dt=0.007000, rms=0.869 (0.014%), neg=0, invalid=1511 0156: dt=0.007000, rms=0.869 (0.018%), neg=0, invalid=1511 0157: dt=0.007000, rms=0.869 (0.020%), neg=0, invalid=1511 0158: dt=0.007000, rms=0.868 (0.019%), neg=0, invalid=1511 0159: dt=0.007000, rms=0.868 (0.021%), neg=0, invalid=1511 0160: dt=0.007000, rms=0.868 (0.024%), neg=0, invalid=1511 0161: dt=0.007000, rms=0.868 (0.024%), neg=0, invalid=1511 0162: dt=0.007000, rms=0.868 (0.026%), neg=0, invalid=1511 0163: dt=0.007000, rms=0.867 (0.027%), neg=0, invalid=1511 0164: dt=0.007000, rms=0.867 (0.028%), neg=0, invalid=1511 0165: dt=0.007000, rms=0.867 (0.028%), neg=0, invalid=1511 0166: dt=0.007000, rms=0.867 (0.030%), neg=0, invalid=1511 0167: dt=0.007000, rms=0.866 (0.031%), neg=0, invalid=1511 0168: dt=0.007000, rms=0.866 (0.030%), neg=0, invalid=1511 0169: dt=0.007000, rms=0.866 (0.030%), neg=0, invalid=1511 0170: dt=0.007000, rms=0.866 (0.031%), neg=0, invalid=1511 0171: dt=0.007000, rms=0.865 (0.030%), neg=0, invalid=1511 0172: dt=0.007000, rms=0.865 (0.029%), neg=0, invalid=1511 0173: dt=0.007000, rms=0.865 (0.030%), neg=0, invalid=1511 0174: dt=0.007000, rms=0.864 (0.028%), neg=0, invalid=1511 0175: dt=0.007000, rms=0.864 (0.028%), neg=0, invalid=1511 0176: dt=0.007000, rms=0.864 (0.025%), neg=0, invalid=1511 0177: dt=0.007000, rms=0.864 (0.025%), neg=0, invalid=1511 0178: dt=0.007000, rms=0.864 (0.023%), neg=0, invalid=1511 0179: dt=0.007000, rms=0.863 (0.023%), neg=0, invalid=1511 0180: dt=0.112000, rms=0.863 (0.021%), neg=0, invalid=1511 0181: dt=0.014000, rms=0.863 (0.002%), neg=0, invalid=1511 0182: dt=0.014000, rms=0.863 (0.004%), neg=0, invalid=1511 0183: dt=0.014000, rms=0.863 (0.007%), neg=0, invalid=1511 0184: dt=0.014000, rms=0.863 (0.006%), neg=0, invalid=1511 0185: dt=0.014000, rms=0.863 (0.009%), neg=0, invalid=1511 0186: dt=0.014000, rms=0.863 (0.011%), neg=0, invalid=1511 0187: dt=0.014000, rms=0.863 (0.011%), neg=0, invalid=1511 0188: dt=0.014000, rms=0.863 (0.012%), neg=0, invalid=1511 0189: dt=0.014000, rms=0.863 (0.013%), neg=0, invalid=1511 0190: dt=0.014000, rms=0.862 (0.014%), neg=0, invalid=1511 0191: dt=0.014000, rms=0.862 (0.014%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.862, neg=0, invalid=1511 0192: dt=0.007000, rms=0.862 (0.006%), neg=0, invalid=1511 0193: dt=0.028000, rms=0.862 (0.026%), neg=0, invalid=1511 0194: dt=0.020000, rms=0.862 (0.017%), neg=0, invalid=1511 0195: dt=0.010000, rms=0.862 (0.010%), neg=0, invalid=1511 0196: dt=0.010000, rms=0.862 (0.017%), neg=0, invalid=1511 0197: dt=0.010000, rms=0.862 (0.022%), neg=0, invalid=1511 0198: dt=0.010000, rms=0.861 (0.030%), neg=0, invalid=1511 0199: dt=0.010000, rms=0.861 (0.034%), neg=0, invalid=1511 0200: dt=0.010000, rms=0.861 (0.040%), neg=0, invalid=1511 0201: dt=0.010000, rms=0.860 (0.044%), neg=0, invalid=1511 0202: dt=0.010000, rms=0.860 (0.046%), neg=0, invalid=1511 0203: dt=0.010000, rms=0.859 (0.049%), neg=0, invalid=1511 0204: dt=0.010000, rms=0.859 (0.051%), neg=0, invalid=1511 0205: dt=0.010000, rms=0.859 (0.052%), neg=0, invalid=1511 0206: dt=0.010000, rms=0.858 (0.052%), neg=0, invalid=1511 0207: dt=0.010000, rms=0.858 (0.055%), neg=0, invalid=1511 0208: dt=0.010000, rms=0.857 (0.055%), neg=0, invalid=1511 0209: dt=0.010000, rms=0.857 (0.055%), neg=0, invalid=1511 0210: dt=0.010000, rms=0.856 (0.055%), neg=0, invalid=1511 0211: dt=0.010000, rms=0.856 (0.054%), neg=0, invalid=1511 0212: dt=0.010000, rms=0.855 (0.056%), neg=0, invalid=1511 0213: dt=0.010000, rms=0.855 (0.054%), neg=0, invalid=1511 0214: dt=0.010000, rms=0.854 (0.053%), neg=0, invalid=1511 0215: dt=0.010000, rms=0.854 (0.052%), neg=0, invalid=1511 0216: dt=0.010000, rms=0.853 (0.052%), neg=0, invalid=1511 0217: dt=0.010000, rms=0.853 (0.050%), neg=0, invalid=1511 0218: dt=0.010000, rms=0.853 (0.050%), neg=0, invalid=1511 0219: dt=0.010000, rms=0.852 (0.048%), neg=0, invalid=1511 0220: dt=0.010000, rms=0.852 (0.046%), neg=0, invalid=1511 0221: dt=0.010000, rms=0.851 (0.044%), neg=0, invalid=1511 0222: dt=0.010000, rms=0.851 (0.044%), neg=0, invalid=1511 0223: dt=0.010000, rms=0.851 (0.042%), neg=0, invalid=1511 0224: dt=0.010000, rms=0.850 (0.041%), neg=0, invalid=1511 0225: dt=0.010000, rms=0.850 (0.037%), neg=0, invalid=1511 0226: dt=0.010000, rms=0.850 (0.037%), neg=0, invalid=1511 0227: dt=0.010000, rms=0.849 (0.035%), neg=0, invalid=1511 0228: dt=0.010000, rms=0.849 (0.035%), neg=0, invalid=1511 0229: dt=0.010000, rms=0.849 (0.033%), neg=0, invalid=1511 0230: dt=0.010000, rms=0.849 (0.032%), neg=0, invalid=1511 0231: dt=0.010000, rms=0.848 (0.030%), neg=0, invalid=1511 0232: dt=0.010000, rms=0.848 (0.029%), neg=0, invalid=1511 0233: dt=0.010000, rms=0.848 (0.027%), neg=0, invalid=1511 0234: dt=0.010000, rms=0.848 (0.026%), neg=0, invalid=1511 0235: dt=0.010000, rms=0.847 (0.026%), neg=0, invalid=1511 0236: dt=0.010000, rms=0.847 (0.024%), neg=0, invalid=1511 0237: dt=0.010000, rms=0.847 (0.022%), neg=0, invalid=1511 0238: dt=0.028000, rms=0.847 (0.005%), neg=0, invalid=1511 0239: dt=0.014000, rms=0.847 (0.003%), neg=0, invalid=1511 0240: dt=0.014000, rms=0.847 (0.003%), neg=0, invalid=1511 0241: dt=0.014000, rms=0.847 (0.005%), neg=0, invalid=1511 0242: dt=0.014000, rms=0.847 (0.006%), neg=0, invalid=1511 0243: dt=0.014000, rms=0.847 (0.007%), neg=0, invalid=1511 0244: dt=0.014000, rms=0.847 (0.008%), neg=0, invalid=1511 0245: dt=0.014000, rms=0.847 (0.010%), neg=0, invalid=1511 0246: dt=0.014000, rms=0.846 (0.011%), neg=0, invalid=1511 0247: dt=0.014000, rms=0.846 (0.011%), neg=0, invalid=1511 0248: dt=0.014000, rms=0.846 (0.012%), neg=0, invalid=1511 0249: dt=0.014000, rms=0.846 (0.013%), neg=0, invalid=1511 0250: dt=0.014000, rms=0.846 (0.013%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.795, neg=0, invalid=1511 0251: dt=0.028000, rms=0.792 (0.404%), neg=0, invalid=1511 0252: dt=0.024000, rms=0.789 (0.334%), neg=0, invalid=1511 0253: dt=0.001750, rms=0.789 (0.022%), neg=0, invalid=1511 0254: dt=0.001750, rms=0.789 (0.024%), neg=0, invalid=1511 0255: dt=0.001750, rms=0.789 (0.045%), neg=0, invalid=1511 0256: dt=0.001750, rms=0.788 (0.064%), neg=0, invalid=1511 0257: dt=0.001750, rms=0.788 (0.083%), neg=0, invalid=1511 0258: dt=0.001750, rms=0.787 (0.023%), neg=0, invalid=1511 0259: dt=0.001750, rms=0.787 (0.045%), neg=0, invalid=1511 0260: dt=0.001750, rms=0.787 (0.023%), neg=0, invalid=1511 0261: dt=0.001750, rms=0.786 (0.045%), neg=0, invalid=1511 0262: dt=0.001750, rms=0.786 (0.063%), neg=0, invalid=1511 0263: dt=0.001750, rms=0.785 (0.079%), neg=0, invalid=1511 0264: dt=0.001750, rms=0.785 (0.023%), neg=0, invalid=1511 0265: dt=0.001750, rms=0.785 (0.043%), neg=0, invalid=1511 0266: dt=0.001750, rms=0.784 (0.062%), neg=0, invalid=1511 0267: dt=0.001750, rms=0.784 (0.078%), neg=0, invalid=1511 0268: dt=0.001750, rms=0.783 (0.093%), neg=0, invalid=1511 0269: dt=0.001750, rms=0.782 (0.107%), neg=0, invalid=1511 0270: dt=0.001750, rms=0.781 (0.118%), neg=0, invalid=1511 0271: dt=0.001750, rms=0.780 (0.127%), neg=0, invalid=1511 0272: dt=0.001750, rms=0.779 (0.136%), neg=0, invalid=1511 0273: dt=0.001750, rms=0.778 (0.143%), neg=0, invalid=1511 0274: dt=0.001750, rms=0.777 (0.149%), neg=0, invalid=1511 0275: dt=0.001750, rms=0.776 (0.154%), neg=0, invalid=1511 0276: dt=0.001750, rms=0.775 (0.159%), neg=0, invalid=1511 0277: dt=0.001750, rms=0.773 (0.162%), neg=0, invalid=1511 0278: dt=0.000875, rms=0.773 (0.009%), neg=0, invalid=1511 0279: dt=0.000875, rms=0.773 (0.018%), neg=0, invalid=1511 0280: dt=0.000875, rms=0.773 (0.010%), neg=0, invalid=1511 0281: dt=0.001750, rms=0.773 (0.019%), neg=0, invalid=1511 0282: dt=0.001750, rms=0.773 (0.019%), neg=0, invalid=1511 0283: dt=0.001750, rms=0.773 (0.018%), neg=0, invalid=1511 0284: dt=0.001750, rms=0.772 (0.018%), neg=0, invalid=1511 0285: dt=0.001750, rms=0.772 (0.036%), neg=0, invalid=1511 0286: dt=0.001750, rms=0.772 (0.051%), neg=0, invalid=1511 0287: dt=0.001750, rms=0.771 (0.063%), neg=0, invalid=1511 0288: dt=0.001750, rms=0.771 (0.077%), neg=0, invalid=1511 0289: dt=0.001750, rms=0.770 (0.088%), neg=0, invalid=1511 0290: dt=0.001750, rms=0.769 (0.096%), neg=0, invalid=1511 0291: dt=0.001750, rms=0.768 (0.106%), neg=0, invalid=1511 0292: dt=0.001750, rms=0.768 (0.111%), neg=0, invalid=1511 0293: dt=0.001750, rms=0.767 (0.117%), neg=0, invalid=1511 0294: dt=0.001750, rms=0.766 (0.125%), neg=0, invalid=1511 0295: dt=0.001750, rms=0.765 (0.128%), neg=0, invalid=1511 0296: dt=0.001750, rms=0.764 (0.131%), neg=0, invalid=1511 0297: dt=0.000875, rms=0.764 (0.008%), neg=0, invalid=1511 0298: dt=0.000875, rms=0.764 (0.008%), neg=0, invalid=1511 0299: dt=0.000438, rms=0.764 (0.004%), neg=0, invalid=1511 0300: dt=0.000438, rms=0.764 (0.003%), neg=0, invalid=1511 0301: dt=0.000438, rms=0.763 (0.009%), neg=0, invalid=1511 0302: dt=0.000438, rms=0.763 (0.010%), neg=0, invalid=1511 0303: dt=0.000438, rms=0.763 (0.013%), neg=0, invalid=1511 0304: dt=0.000438, rms=0.763 (0.016%), neg=0, invalid=1511 0305: dt=0.000438, rms=0.763 (0.020%), neg=0, invalid=1511 0306: dt=0.000438, rms=0.763 (0.021%), neg=0, invalid=1511 0307: dt=0.000438, rms=0.763 (0.021%), neg=0, invalid=1511 0308: dt=0.000438, rms=0.763 (0.024%), neg=0, invalid=1511 0309: dt=0.000438, rms=0.762 (0.004%), neg=0, invalid=1511 0310: dt=0.000438, rms=0.762 (0.008%), neg=0, invalid=1511 0311: dt=0.000438, rms=0.762 (0.011%), neg=0, invalid=1511 0312: dt=0.000438, rms=0.762 (0.014%), neg=0, invalid=1511 0313: dt=0.000438, rms=0.762 (0.015%), neg=0, invalid=1511 0314: dt=0.000438, rms=0.762 (0.019%), neg=0, invalid=1511 0315: dt=0.000438, rms=0.762 (0.020%), neg=0, invalid=1511 0316: dt=0.000438, rms=0.762 (0.022%), neg=0, invalid=1511 0317: dt=0.000438, rms=0.761 (0.025%), neg=0, invalid=1511 0318: dt=0.000438, rms=0.761 (0.025%), neg=0, invalid=1511 0319: dt=0.000438, rms=0.761 (0.027%), neg=0, invalid=1511 0320: dt=0.000438, rms=0.761 (0.028%), neg=0, invalid=1511 0321: dt=0.000438, rms=0.761 (0.029%), neg=0, invalid=1511 0322: dt=0.000438, rms=0.760 (0.030%), neg=0, invalid=1511 0323: dt=0.000438, rms=0.760 (0.030%), neg=0, invalid=1511 0324: dt=0.000438, rms=0.760 (0.031%), neg=0, invalid=1511 0325: dt=0.000438, rms=0.760 (0.033%), neg=0, invalid=1511 0326: dt=0.000438, rms=0.759 (0.032%), neg=0, invalid=1511 0327: dt=0.000438, rms=0.759 (0.032%), neg=0, invalid=1511 0328: dt=0.000438, rms=0.759 (0.035%), neg=0, invalid=1511 0329: dt=0.000438, rms=0.759 (0.034%), neg=0, invalid=1511 0330: dt=0.000438, rms=0.758 (0.034%), neg=0, invalid=1511 0331: dt=0.000438, rms=0.758 (0.033%), neg=0, invalid=1511 0332: dt=0.000438, rms=0.758 (0.036%), neg=0, invalid=1511 0333: dt=0.000438, rms=0.758 (0.035%), neg=0, invalid=1511 0334: dt=0.000438, rms=0.757 (0.036%), neg=0, invalid=1511 0335: dt=0.000438, rms=0.757 (0.034%), neg=0, invalid=1511 0336: dt=0.000438, rms=0.757 (0.036%), neg=0, invalid=1511 0337: dt=0.000438, rms=0.757 (0.034%), neg=0, invalid=1511 0338: dt=0.000438, rms=0.756 (0.035%), neg=0, invalid=1511 0339: dt=0.000438, rms=0.756 (0.034%), neg=0, invalid=1511 0340: dt=0.000438, rms=0.756 (0.037%), neg=0, invalid=1511 0341: dt=0.000438, rms=0.756 (0.035%), neg=0, invalid=1511 0342: dt=0.000438, rms=0.755 (0.035%), neg=0, invalid=1511 0343: dt=0.000438, rms=0.755 (0.034%), neg=0, invalid=1511 0344: dt=0.000438, rms=0.755 (0.035%), neg=0, invalid=1511 0345: dt=0.000438, rms=0.754 (0.035%), neg=0, invalid=1511 0346: dt=0.000438, rms=0.754 (0.036%), neg=0, invalid=1511 0347: dt=0.000438, rms=0.754 (0.034%), neg=0, invalid=1511 0348: dt=0.000438, rms=0.754 (0.035%), neg=0, invalid=1511 0349: dt=0.000438, rms=0.753 (0.034%), neg=0, invalid=1511 0350: dt=0.000438, rms=0.753 (0.033%), neg=0, invalid=1511 0351: dt=0.000438, rms=0.753 (0.035%), neg=0, invalid=1511 0352: dt=0.000438, rms=0.753 (0.033%), neg=0, invalid=1511 0353: dt=0.000438, rms=0.752 (0.033%), neg=0, invalid=1511 0354: dt=0.000438, rms=0.752 (0.033%), neg=0, invalid=1511 0355: dt=0.000438, rms=0.752 (0.033%), neg=0, invalid=1511 0356: dt=0.000438, rms=0.752 (0.033%), neg=0, invalid=1511 0357: dt=0.000438, rms=0.751 (0.033%), neg=0, invalid=1511 0358: dt=0.000438, rms=0.751 (0.033%), neg=0, invalid=1511 0359: dt=0.000438, rms=0.751 (0.032%), neg=0, invalid=1511 0360: dt=0.000438, rms=0.751 (0.032%), neg=0, invalid=1511 0361: dt=0.000438, rms=0.750 (0.034%), neg=0, invalid=1511 0362: dt=0.000438, rms=0.750 (0.032%), neg=0, invalid=1511 0363: dt=0.000438, rms=0.750 (0.031%), neg=0, invalid=1511 0364: dt=0.000438, rms=0.750 (0.032%), neg=0, invalid=1511 0365: dt=0.000438, rms=0.750 (0.031%), neg=0, invalid=1511 0366: dt=0.000438, rms=0.749 (0.032%), neg=0, invalid=1511 0367: dt=0.000438, rms=0.749 (0.032%), neg=0, invalid=1511 0368: dt=0.000438, rms=0.749 (0.031%), neg=0, invalid=1511 0369: dt=0.000438, rms=0.749 (0.031%), neg=0, invalid=1511 0370: dt=0.000438, rms=0.748 (0.031%), neg=0, invalid=1511 0371: dt=0.000438, rms=0.748 (0.031%), neg=0, invalid=1511 0372: dt=0.000438, rms=0.748 (0.030%), neg=0, invalid=1511 0373: dt=0.000438, rms=0.748 (0.030%), neg=0, invalid=1511 0374: dt=0.000438, rms=0.747 (0.030%), neg=0, invalid=1511 0375: dt=0.000438, rms=0.747 (0.029%), neg=0, invalid=1511 0376: dt=0.000438, rms=0.747 (0.029%), neg=0, invalid=1511 0377: dt=0.000438, rms=0.747 (0.030%), neg=0, invalid=1511 0378: dt=0.000438, rms=0.747 (0.030%), neg=0, invalid=1511 0379: dt=0.000438, rms=0.746 (0.029%), neg=0, invalid=1511 0380: dt=0.000438, rms=0.746 (0.029%), neg=0, invalid=1511 0381: dt=0.000438, rms=0.746 (0.028%), neg=0, invalid=1511 0382: dt=0.000438, rms=0.746 (0.029%), neg=0, invalid=1511 0383: dt=0.000438, rms=0.745 (0.029%), neg=0, invalid=1511 0384: dt=0.000438, rms=0.745 (0.029%), neg=0, invalid=1511 0385: dt=0.000438, rms=0.745 (0.029%), neg=0, invalid=1511 0386: dt=0.000438, rms=0.745 (0.027%), neg=0, invalid=1511 0387: dt=0.000438, rms=0.745 (0.028%), neg=0, invalid=1511 0388: dt=0.000438, rms=0.744 (0.029%), neg=0, invalid=1511 0389: dt=0.000438, rms=0.744 (0.029%), neg=0, invalid=1511 0390: dt=0.000438, rms=0.744 (0.027%), neg=0, invalid=1511 0391: dt=0.000438, rms=0.744 (0.025%), neg=0, invalid=1511 0392: dt=0.000438, rms=0.744 (0.026%), neg=0, invalid=1511 0393: dt=0.000438, rms=0.743 (0.028%), neg=0, invalid=1511 0394: dt=0.000438, rms=0.743 (0.026%), neg=0, invalid=1511 0395: dt=0.000438, rms=0.743 (0.027%), neg=0, invalid=1511 0396: dt=0.000438, rms=0.743 (0.027%), neg=0, invalid=1511 0397: dt=0.000438, rms=0.743 (0.027%), neg=0, invalid=1511 0398: dt=0.000438, rms=0.742 (0.026%), neg=0, invalid=1511 0399: dt=0.000438, rms=0.742 (0.026%), neg=0, invalid=1511 0400: dt=0.000438, rms=0.742 (0.026%), neg=0, invalid=1511 0401: dt=0.000438, rms=0.742 (0.026%), neg=0, invalid=1511 0402: dt=0.000438, rms=0.742 (0.027%), neg=0, invalid=1511 0403: dt=0.000438, rms=0.741 (0.025%), neg=0, invalid=1511 0404: dt=0.000438, rms=0.741 (0.026%), neg=0, invalid=1511 0405: dt=0.000438, rms=0.741 (0.025%), neg=0, invalid=1511 0406: dt=0.000438, rms=0.741 (0.025%), neg=0, invalid=1511 0407: dt=0.000438, rms=0.741 (0.025%), neg=0, invalid=1511 0408: dt=0.000438, rms=0.741 (0.026%), neg=0, invalid=1511 0409: dt=0.000438, rms=0.740 (0.025%), neg=0, invalid=1511 0410: dt=0.000438, rms=0.740 (0.024%), neg=0, invalid=1511 0411: dt=0.000438, rms=0.740 (0.025%), neg=0, invalid=1511 0412: dt=0.000438, rms=0.740 (0.023%), neg=0, invalid=1511 0413: dt=0.028000, rms=0.739 (0.148%), neg=0, invalid=1511 0414: dt=0.001750, rms=0.739 (0.009%), neg=0, invalid=1511 0415: dt=0.000875, rms=0.739 (0.005%), neg=0, invalid=1511 0416: dt=0.000875, rms=0.739 (0.005%), neg=0, invalid=1511 0417: dt=0.000875, rms=0.739 (0.004%), neg=0, invalid=1511 0418: dt=0.000438, rms=0.739 (0.003%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.739, neg=0, invalid=1511 0419: dt=0.000438, rms=0.738 (0.003%), neg=0, invalid=1511 0420: dt=0.001500, rms=0.738 (0.012%), neg=0, invalid=1511 0421: dt=0.000438, rms=0.738 (0.004%), neg=0, invalid=1511 0422: dt=0.000438, rms=0.738 (0.003%), neg=0, invalid=1511 0423: dt=0.000438, rms=0.738 (0.007%), neg=0, invalid=1511 0424: dt=0.000438, rms=0.738 (0.010%), neg=0, invalid=1511 0425: dt=0.000438, rms=0.738 (0.004%), neg=0, invalid=1511 0426: dt=0.000438, rms=0.738 (0.007%), neg=0, invalid=1511 0427: dt=0.000438, rms=0.738 (0.010%), neg=0, invalid=1511 0428: dt=0.000438, rms=0.738 (0.012%), neg=0, invalid=1511 0429: dt=0.000438, rms=0.738 (0.014%), neg=0, invalid=1511 0430: dt=0.000438, rms=0.738 (0.017%), neg=0, invalid=1511 0431: dt=0.000438, rms=0.738 (0.018%), neg=0, invalid=1511 0432: dt=0.000438, rms=0.737 (0.021%), neg=0, invalid=1511 0433: dt=0.000438, rms=0.737 (0.020%), neg=0, invalid=1511 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 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.736, neg=0, invalid=1511 0434: dt=2.023000, rms=0.734 (0.252%), neg=0, invalid=1511 0435: dt=2.023000, rms=0.733 (0.239%), neg=0, invalid=1511 0436: dt=0.505750, rms=0.732 (0.046%), neg=0, invalid=1511 0437: dt=0.505750, rms=0.732 (0.041%), neg=0, invalid=1511 0438: dt=0.126438, rms=0.732 (0.009%), neg=0, invalid=1511 0439: dt=0.031609, rms=0.732 (0.002%), neg=0, invalid=1511 0440: dt=0.020230, rms=0.732 (0.001%), neg=0, invalid=1511 0441: dt=0.001264, rms=0.732 (0.000%), neg=0, invalid=1511 0442: dt=0.000079, rms=0.732 (0.000%), neg=0, invalid=1511 0443: dt=0.000040, rms=0.732 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.732, neg=0, invalid=1511 0444: dt=0.000000, rms=0.732 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.732, neg=0, invalid=1511 0445: dt=0.486000, rms=0.730 (0.221%), neg=0, invalid=1511 0446: dt=0.025313, rms=0.730 (0.009%), neg=0, invalid=1511 0447: dt=0.003164, rms=0.730 (0.001%), neg=0, invalid=1511 0448: dt=0.000791, rms=0.730 (0.000%), neg=0, invalid=1511 0449: dt=0.000099, rms=0.730 (0.000%), neg=0, invalid=1511 0450: dt=0.000000, rms=0.730 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=1511 0451: dt=0.000000, rms=0.730 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.730, neg=0, invalid=1511 0452: dt=0.000000, rms=0.730 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=1511 0453: dt=0.000000, rms=0.730 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.730, neg=0, invalid=1511 0454: dt=0.000000, rms=0.730 (0.000%), neg=0, invalid=1511 0455: dt=0.000009, rms=0.730 (0.000%), neg=0, invalid=1511 0456: dt=0.000005, rms=0.730 (0.000%), neg=0, invalid=1511 0457: dt=0.000002, rms=0.730 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.730, neg=0, invalid=1511 0458: dt=0.000000, rms=0.730 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.731, neg=0, invalid=1511 0459: dt=0.006000, rms=0.731 (0.008%), neg=0, invalid=1511 0460: dt=0.005000, rms=0.731 (0.017%), neg=0, invalid=1511 0461: dt=0.005000, rms=0.730 (0.016%), neg=0, invalid=1511 0462: dt=0.005000, rms=0.730 (0.018%), neg=0, invalid=1511 0463: dt=0.002500, rms=0.730 (0.009%), neg=0, invalid=1511 0464: dt=0.002500, rms=0.730 (0.018%), neg=0, invalid=1511 0465: dt=0.002500, rms=0.730 (0.025%), neg=0, invalid=1511 0466: dt=0.002500, rms=0.730 (0.033%), neg=0, invalid=1511 0467: dt=0.002500, rms=0.729 (0.039%), neg=0, invalid=1511 0468: dt=0.002500, rms=0.729 (0.045%), neg=0, invalid=1511 0469: dt=0.002500, rms=0.729 (0.051%), neg=0, invalid=1511 0470: dt=0.002500, rms=0.728 (0.056%), neg=0, invalid=1511 0471: dt=0.002500, rms=0.728 (0.061%), neg=0, invalid=1511 0472: dt=0.002500, rms=0.727 (0.065%), neg=0, invalid=1511 0473: dt=0.002500, rms=0.727 (0.069%), neg=0, invalid=1511 0474: dt=0.002500, rms=0.726 (0.072%), neg=0, invalid=1511 0475: dt=0.002500, rms=0.726 (0.075%), neg=0, invalid=1511 0476: dt=0.002500, rms=0.725 (0.077%), neg=0, invalid=1511 0477: dt=0.002500, rms=0.725 (0.079%), neg=0, invalid=1511 0478: dt=0.002500, rms=0.724 (0.080%), neg=0, invalid=1511 0479: dt=0.002500, rms=0.724 (0.009%), neg=0, invalid=1511 0480: dt=0.002500, rms=0.724 (0.017%), neg=0, invalid=1511 0481: dt=0.002500, rms=0.724 (0.024%), neg=0, invalid=1511 0482: dt=0.002500, rms=0.724 (0.031%), neg=0, invalid=1511 0483: dt=0.002500, rms=0.723 (0.037%), neg=0, invalid=1511 0484: dt=0.002500, rms=0.723 (0.042%), neg=0, invalid=1511 0485: dt=0.002500, rms=0.723 (0.046%), neg=0, invalid=1511 0486: dt=0.002500, rms=0.722 (0.050%), neg=0, invalid=1511 0487: dt=0.002500, rms=0.722 (0.053%), neg=0, invalid=1511 0488: dt=0.002500, rms=0.721 (0.056%), neg=0, invalid=1511 0489: dt=0.002500, rms=0.721 (0.058%), neg=0, invalid=1511 0490: dt=0.002500, rms=0.721 (0.060%), neg=0, invalid=1511 0491: dt=0.002500, rms=0.720 (0.062%), neg=0, invalid=1511 0492: dt=0.002500, rms=0.720 (0.063%), neg=0, invalid=1511 0493: dt=0.002500, rms=0.719 (0.064%), neg=0, invalid=1511 0494: dt=0.002500, rms=0.719 (0.064%), neg=0, invalid=1511 0495: dt=0.002500, rms=0.718 (0.065%), neg=0, invalid=1511 0496: dt=0.002500, rms=0.718 (0.065%), neg=0, invalid=1511 0497: dt=0.002500, rms=0.717 (0.065%), neg=0, invalid=1511 0498: dt=0.002500, rms=0.717 (0.065%), neg=0, invalid=1511 0499: dt=0.002500, rms=0.716 (0.065%), neg=0, invalid=1511 0500: dt=0.002500, rms=0.716 (0.065%), neg=0, invalid=1511 0501: dt=0.002500, rms=0.716 (0.064%), neg=0, invalid=1511 0502: dt=0.002500, rms=0.715 (0.063%), neg=0, invalid=1511 0503: dt=0.002500, rms=0.715 (0.063%), neg=0, invalid=1511 0504: dt=0.002500, rms=0.714 (0.062%), neg=0, invalid=1511 0505: dt=0.002500, rms=0.714 (0.061%), neg=0, invalid=1511 0506: dt=0.002500, rms=0.713 (0.060%), neg=0, invalid=1511 0507: dt=0.002500, rms=0.713 (0.059%), neg=0, invalid=1511 0508: dt=0.002500, rms=0.712 (0.058%), neg=0, invalid=1511 0509: dt=0.002500, rms=0.712 (0.057%), neg=0, invalid=1511 0510: dt=0.002500, rms=0.712 (0.056%), neg=0, invalid=1511 0511: dt=0.002500, rms=0.711 (0.055%), neg=0, invalid=1511 0512: dt=0.002500, rms=0.711 (0.054%), neg=0, invalid=1511 0513: dt=0.002500, rms=0.711 (0.053%), neg=0, invalid=1511 0514: dt=0.002500, rms=0.710 (0.052%), neg=0, invalid=1511 0515: dt=0.002500, rms=0.710 (0.051%), neg=0, invalid=1511 0516: dt=0.002500, rms=0.709 (0.050%), neg=0, invalid=1511 0517: dt=0.002500, rms=0.709 (0.049%), neg=0, invalid=1511 0518: dt=0.002500, rms=0.709 (0.048%), neg=0, invalid=1511 0519: dt=0.002500, rms=0.708 (0.047%), neg=0, invalid=1511 0520: dt=0.002500, rms=0.708 (0.046%), neg=0, invalid=1511 0521: dt=0.002500, rms=0.708 (0.045%), neg=0, invalid=1511 0522: dt=0.002500, rms=0.707 (0.044%), neg=0, invalid=1511 0523: dt=0.002500, rms=0.707 (0.043%), neg=0, invalid=1511 0524: dt=0.002500, rms=0.707 (0.042%), neg=0, invalid=1511 0525: dt=0.002500, rms=0.707 (0.042%), neg=0, invalid=1511 0526: dt=0.002500, rms=0.706 (0.041%), neg=0, invalid=1511 0527: dt=0.002500, rms=0.706 (0.040%), neg=0, invalid=1511 0528: dt=0.002500, rms=0.706 (0.039%), neg=0, invalid=1511 0529: dt=0.002500, rms=0.705 (0.039%), neg=0, invalid=1511 0530: dt=0.002500, rms=0.705 (0.038%), neg=0, invalid=1511 0531: dt=0.002500, rms=0.705 (0.037%), neg=0, invalid=1511 0532: dt=0.002500, rms=0.705 (0.036%), neg=0, invalid=1511 0533: dt=0.002500, rms=0.704 (0.036%), neg=0, invalid=1511 0534: dt=0.002500, rms=0.704 (0.035%), neg=0, invalid=1511 0535: dt=0.002500, rms=0.704 (0.034%), neg=0, invalid=1511 0536: dt=0.002500, rms=0.704 (0.034%), neg=0, invalid=1511 0537: dt=0.002500, rms=0.703 (0.033%), neg=0, invalid=1511 0538: dt=0.002500, rms=0.703 (0.032%), neg=0, invalid=1511 0539: dt=0.002500, rms=0.703 (0.032%), neg=0, invalid=1511 0540: dt=0.002500, rms=0.703 (0.031%), neg=0, invalid=1511 0541: dt=0.002500, rms=0.703 (0.031%), neg=0, invalid=1511 0542: dt=0.002500, rms=0.702 (0.030%), neg=0, invalid=1511 0543: dt=0.002500, rms=0.702 (0.029%), neg=0, invalid=1511 0544: dt=0.002500, rms=0.702 (0.029%), neg=0, invalid=1511 0545: dt=0.002500, rms=0.702 (0.028%), neg=0, invalid=1511 0546: dt=0.002500, rms=0.702 (0.028%), neg=0, invalid=1511 0547: dt=0.002500, rms=0.701 (0.027%), neg=0, invalid=1511 0548: dt=0.002500, rms=0.701 (0.027%), neg=0, invalid=1511 0549: dt=0.002500, rms=0.701 (0.026%), neg=0, invalid=1511 0550: dt=0.002500, rms=0.701 (0.026%), neg=0, invalid=1511 0551: dt=0.002500, rms=0.701 (0.025%), neg=0, invalid=1511 0552: dt=0.002500, rms=0.700 (0.025%), neg=0, invalid=1511 0553: dt=0.002500, rms=0.700 (0.025%), neg=0, invalid=1511 0554: dt=0.002500, rms=0.700 (0.024%), neg=0, invalid=1511 0555: dt=0.112000, rms=0.699 (0.091%), neg=0, invalid=1511 0556: dt=0.006410, rms=0.699 (0.005%), neg=0, invalid=1511 0557: dt=0.006410, rms=0.699 (0.003%), neg=0, invalid=1511 0558: dt=0.003205, rms=0.699 (0.002%), neg=0, invalid=1511 0559: dt=0.003205, rms=0.699 (0.004%), neg=0, invalid=1511 0560: dt=0.003205, rms=0.699 (0.002%), neg=0, invalid=1511 0561: dt=0.006000, rms=0.699 (0.004%), neg=0, invalid=1511 0562: dt=0.006000, rms=0.699 (0.003%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.699, neg=0, invalid=1511 0563: dt=0.001750, rms=0.699 (0.003%), neg=0, invalid=1511 0564: dt=0.006000, rms=0.699 (0.010%), neg=0, invalid=1511 0565: dt=0.001750, rms=0.699 (0.003%), neg=0, invalid=1511 0566: dt=0.001750, rms=0.699 (0.003%), neg=0, invalid=1511 0567: dt=0.001750, rms=0.699 (0.006%), neg=0, invalid=1511 0568: dt=0.001750, rms=0.699 (0.008%), neg=0, invalid=1511 0569: dt=0.001750, rms=0.699 (0.010%), neg=0, invalid=1511 0570: dt=0.001750, rms=0.699 (0.012%), neg=0, invalid=1511 0571: dt=0.001750, rms=0.699 (0.014%), neg=0, invalid=1511 0572: dt=0.001750, rms=0.699 (0.015%), neg=0, invalid=1511 0573: dt=0.001750, rms=0.699 (0.017%), neg=0, invalid=1511 0574: dt=0.001750, rms=0.698 (0.018%), neg=0, invalid=1511 0575: dt=0.001750, rms=0.698 (0.019%), neg=0, invalid=1511 0576: dt=0.001750, rms=0.698 (0.020%), neg=0, invalid=1511 0577: dt=0.001750, rms=0.698 (0.021%), neg=0, invalid=1511 0578: dt=0.001750, rms=0.698 (0.021%), neg=0, invalid=1511 0579: dt=0.001750, rms=0.698 (0.022%), neg=0, invalid=1511 0580: dt=0.001750, rms=0.698 (0.023%), neg=0, invalid=1511 0581: dt=0.001750, rms=0.697 (0.023%), neg=0, invalid=1511 0582: dt=0.001750, rms=0.697 (0.024%), neg=0, invalid=1511 0583: dt=0.001750, rms=0.697 (0.024%), neg=0, invalid=1511 0584: dt=0.001750, rms=0.697 (0.024%), neg=0, invalid=1511 0585: dt=0.001750, rms=0.697 (0.024%), neg=0, invalid=1511 0586: dt=0.001750, rms=0.697 (0.025%), neg=0, invalid=1511 0587: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0588: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0589: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0590: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0591: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0592: dt=0.001750, rms=0.696 (0.025%), neg=0, invalid=1511 0593: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0594: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0595: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0596: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0597: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0598: dt=0.001750, rms=0.695 (0.025%), neg=0, invalid=1511 0599: dt=0.001750, rms=0.694 (0.025%), neg=0, invalid=1511 0600: dt=0.020000, rms=0.694 (0.027%), neg=0, invalid=1511 0601: dt=0.005000, rms=0.694 (0.006%), neg=0, invalid=1511 0602: dt=0.005000, rms=0.694 (0.006%), neg=0, invalid=1511 0603: dt=0.002500, rms=0.694 (0.003%), neg=0, invalid=1511 0604: dt=0.002500, rms=0.694 (0.006%), neg=0, invalid=1511 0605: dt=0.002500, rms=0.694 (0.003%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.692, neg=0, invalid=1511 0606: dt=0.007000, rms=0.692 (0.079%), neg=0, invalid=1511 0607: dt=0.007000, rms=0.691 (0.078%), neg=0, invalid=1511 0608: dt=0.001750, rms=0.691 (0.019%), neg=0, invalid=1511 0609: dt=0.000875, rms=0.691 (0.010%), neg=0, invalid=1511 0610: dt=0.000875, rms=0.691 (0.018%), neg=0, invalid=1511 0611: dt=0.000875, rms=0.690 (0.026%), neg=0, invalid=1511 0612: dt=0.000875, rms=0.690 (0.010%), neg=0, invalid=1511 0613: dt=0.000875, rms=0.690 (0.010%), neg=0, invalid=1511 0614: dt=0.001250, rms=0.690 (0.014%), neg=0, invalid=1511 0615: dt=0.001750, rms=0.690 (0.019%), neg=0, invalid=1511 0616: dt=0.001500, rms=0.690 (0.016%), neg=0, invalid=1511 0617: dt=0.001500, rms=0.690 (0.016%), neg=0, invalid=1511 0618: dt=0.001500, rms=0.690 (0.030%), neg=0, invalid=1511 0619: dt=0.001500, rms=0.690 (0.016%), neg=0, invalid=1511 0620: dt=0.001500, rms=0.689 (0.030%), neg=0, invalid=1511 0621: dt=0.001500, rms=0.689 (0.043%), neg=0, invalid=1511 0622: dt=0.001500, rms=0.689 (0.015%), neg=0, invalid=1511 0623: dt=0.000375, rms=0.689 (0.004%), neg=0, invalid=1511 0624: dt=0.000438, rms=0.689 (0.004%), neg=0, invalid=1511 0625: dt=0.001750, rms=0.689 (0.018%), neg=0, invalid=1511 0626: dt=0.000438, rms=0.689 (0.004%), neg=0, invalid=1511 0627: dt=0.000438, rms=0.689 (0.004%), neg=0, invalid=1511 0628: dt=0.000438, rms=0.689 (0.008%), neg=0, invalid=1511 0629: dt=0.000438, rms=0.689 (0.012%), neg=0, invalid=1511 0630: dt=0.000438, rms=0.688 (0.015%), neg=0, invalid=1511 0631: dt=0.000438, rms=0.688 (0.018%), neg=0, invalid=1511 0632: dt=0.000438, rms=0.688 (0.004%), neg=0, invalid=1511 0633: dt=0.000438, rms=0.688 (0.008%), neg=0, invalid=1511 0634: dt=0.000438, rms=0.688 (0.012%), neg=0, invalid=1511 0635: dt=0.000438, rms=0.688 (0.004%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.688, neg=0, invalid=1511 0636: dt=0.001750, rms=0.688 (0.023%), neg=0, invalid=1511 0637: dt=0.000438, rms=0.688 (0.006%), neg=0, invalid=1511 0638: dt=0.000438, rms=0.688 (0.006%), neg=0, invalid=1511 0639: dt=0.000438, rms=0.688 (0.011%), neg=0, invalid=1511 0640: dt=0.000438, rms=0.688 (0.015%), neg=0, invalid=1511 0641: dt=0.000438, rms=0.688 (0.019%), neg=0, invalid=1511 0642: dt=0.000438, rms=0.687 (0.023%), neg=0, invalid=1511 0643: dt=0.000438, rms=0.687 (0.026%), neg=0, invalid=1511 0644: dt=0.000438, rms=0.687 (0.029%), neg=0, invalid=1511 0645: dt=0.000438, rms=0.687 (0.032%), neg=0, invalid=1511 0646: dt=0.000438, rms=0.687 (0.034%), neg=0, invalid=1511 0647: dt=0.000438, rms=0.686 (0.036%), neg=0, invalid=1511 0648: dt=0.000438, rms=0.686 (0.037%), neg=0, invalid=1511 0649: dt=0.000438, rms=0.686 (0.039%), neg=0, invalid=1511 0650: dt=0.000438, rms=0.686 (0.005%), neg=0, invalid=1511 0651: dt=0.000438, rms=0.686 (0.010%), neg=0, invalid=1511 0652: dt=0.000438, rms=0.686 (0.005%), neg=0, invalid=1511 0653: dt=0.001750, rms=0.686 (0.020%), neg=0, invalid=1511 0654: dt=0.000313, rms=0.686 (0.004%), neg=0, invalid=1511 0655: dt=0.000313, rms=0.686 (0.004%), neg=0, invalid=1511 0656: dt=0.000313, rms=0.685 (0.007%), neg=0, invalid=1511 0657: dt=0.000313, rms=0.685 (0.004%), neg=0, invalid=1511 0658: dt=0.000313, rms=0.685 (0.007%), neg=0, invalid=1511 0659: dt=0.000313, rms=0.685 (0.004%), neg=0, invalid=1511 writing output transformation to transforms/talairach.m3z... CA registration took 7 hours, 28 minutes and 3 seconds. #-------------------------------------- #@# CA Reg Inv Tue Oct 16 22:54:03 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z gcam->type = vox reading labels out of gcam file... Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Tue Oct 16 23:01:12 CDT 2007 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... gcam->type = vox reading labels out of gcam file... removing structures at least 25 mm from brain... 15918791 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 7 minutes and 24 seconds. #-------------------------------------- #@# SkullLTA Tue Oct 16 23:08:36 CDT 2007 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_withskull_2006-02-15.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 '/pkg/brainmap/freesurfer-v3.0.5/average/RB_all_withskull_2006-02-15.gca'... setting gca type = Normal gca type average std = 23.5 using min determinant for regularization = 55.2 0 singular and 6473 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... total sample mean = 91.1 (1456 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 3516, passno 0, spacing 8 Result so far: scale 1.000: max_log_p=-20029.3, old_max_log_p =-41340.3 (thresh=-41299.0) -2.666 0.484 -1.603 920.784; 1.136 -1.538 -2.510 650.878; -1.041 -3.020 1.003 421.303; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-19385.2, old_max_log_p =-20029.3 (thresh=-20009.3) -3.238 -0.001 -1.913 1165.076; 1.451 -1.164 -2.706 595.434; -0.598 -3.874 1.024 450.909; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-19061.9, old_max_log_p =-19385.2 (thresh=-19365.8) -3.918 -1.278 -1.861 1449.299; 1.580 -1.844 -2.595 629.736; 0.161 -4.235 2.190 97.519; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-18870.0, old_max_log_p =-19061.9 (thresh=-19042.9) -4.256 -0.495 -1.947 1438.005; 0.805 -1.810 -2.747 807.692; -0.461 -5.225 2.282 316.020; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-18829.0, old_max_log_p =-18870.0 (thresh=-18851.2) -4.359 -0.789 -2.454 1607.852; 1.477 -1.831 -2.602 649.411; -0.432 -4.899 2.140 302.936; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-18602.0, old_max_log_p =-18829.0 (thresh=-18810.2) -5.054 0.485 -2.164 1537.176; 0.245 -2.225 -3.575 1151.949; -1.276 -5.841 2.260 538.242; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-18517.6, old_max_log_p =-18602.0 (thresh=-18583.4) -5.129 1.373 -2.611 1546.981; 0.260 -2.364 -3.798 1223.823; -2.090 -6.074 2.057 776.965; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-18213.7, old_max_log_p =-18517.6 (thresh=-18499.1) -6.368 0.116 -3.210 2098.499; 1.318 -1.539 -4.628 1110.784; -1.275 -7.811 2.164 800.048; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-17980.1, old_max_log_p =-18213.7 (thresh=-18195.5) -7.823 -0.968 -3.145 2515.477; 1.046 -3.161 -5.244 1500.753; -0.673 -8.924 3.824 429.501; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-17723.3, old_max_log_p =-17980.1 (thresh=-17962.1) -8.509 -4.937 -3.990 3337.650; 3.516 -3.443 -4.061 772.936; 1.059 -7.938 5.125 -331.238; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-17532.6, old_max_log_p =-17723.3 (thresh=-17705.6) -8.617 -8.688 -3.807 3776.628; 4.517 -3.574 -2.531 240.413; 2.879 -6.388 6.663 -1221.783; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-17502.2, old_max_log_p =-17532.6 (thresh=-17515.0) -10.719 -8.288 -3.332 4022.153; 1.967 -5.830 -3.482 1227.149; 3.239 -7.187 7.496 -1402.841; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-17502.2, old_max_log_p =-17502.2 (thresh=-17484.7) -10.719 -8.288 -3.332 4022.153; 1.967 -5.830 -3.482 1227.149; 3.239 -7.187 7.496 -1402.841; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix -10.71932 -8.28760 -3.33214 4022.15259; 1.96722 -5.83036 -3.48247 1227.14880; 3.23859 -7.18685 7.49594 -1402.84058; 0.00000 0.00000 0.00000 1.00000; nsamples 3516 Quasinewton: input matrix -10.71932 -8.28760 -3.33214 4022.15259; 1.96722 -5.83036 -3.48247 1227.14880; 3.23859 -7.18685 7.49594 -1402.84058; 0.00000 0.00000 0.00000 1.00000; fp = 17500.451172, fret = 17500.394531, ftol = 0.000010, EPS = 0.000000 pass 2 through quasi-newton minimization... fp = 17500.451172, fret = 17500.394531, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix -10.71932 -8.28760 -3.33214 4022.15259; 1.96722 -5.83036 -3.48247 1227.14880; 3.23859 -7.18685 7.49594 -1402.84058; 0.00000 0.00000 0.00000 1.00000; nsamples 385836 Quasinewton: input matrix -10.71932 -8.28760 -3.33214 4022.15259; 1.96722 -5.83036 -3.48247 1227.14880; 3.23859 -7.18685 7.49594 -1402.84058; 0.00000 0.00000 0.00000 1.00000; freeing gibbs priors...done. bounding unknown intensity as < 20.7 or > 1320.6 ************************************************ spacing=8, using 3516 sample points, tol=1.00e-05... ************************************************ resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 73 --> 73 input volume #1 is the most T1-like using real data threshold=14.0 using (154, 86, 204) as brain centroid... mean wm in atlas = 126, using box (144,73,196) --> (163, 98,212) to find MRI wm before smoothing, mri peak at 19 after smoothing, mri peak at 19, scaling input intensities by 6.632 scaling channel 0 by 6.63158 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** **************************************** Nine parameter search. iteration 3 nscales = 3 ... **************************************** **************************************** Nine parameter search. iteration 4 nscales = 4 ... **************************************** **************************************** Nine parameter search. iteration 5 nscales = 5 ... **************************************** **************************************** Nine parameter search. iteration 6 nscales = 6 ... **************************************** **************************************** Nine parameter search. iteration 7 nscales = 7 ... **************************************** **************************************** Nine parameter search. iteration 8 nscales = 8 ... **************************************** **************************************** Nine parameter search. iteration 9 nscales = 9 ... **************************************** **************************************** Nine parameter search. iteration 10 nscales = 10 ... **************************************** **************************************** Nine parameter search. iteration 11 nscales = 11 ... **************************************** **************************************** Nine parameter search. iteration 12 nscales = 12 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 3516 samples... *********************************************** dfp_em_step_func: 013: -log(p) = 17502.2 after pass:transform: ( -10.72, -8.29, -3.33, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.24, -7.19, 7.50, -1402.84) dfp_em_step_func: 014: -log(p) = 17500.5 after pass:transform: ( -10.72, -8.29, -3.33, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.24, -7.19, 7.50, -1402.84) dfp_em_step_func: 015: -log(p) = 17500.4 after pass:transform: ( -10.72, -8.29, -3.33, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.24, -7.19, 7.50, -1402.84) outof QuasiNewtonEMA: 017: -log(p) = 17500.5 tol 0.000010 Resulting transform: -10.719 -8.288 -3.332 4022.153; 1.967 -5.830 -3.482 1227.149; 3.239 -7.187 7.496 -1402.841; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -17502.2 (old=-41340.3) transform before final EM align: -10.719 -8.288 -3.332 4022.153; 1.967 -5.830 -3.482 1227.149; 3.239 -7.187 7.496 -1402.841; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 385836 samples. ************************************************** dfp_em_step_func: 016: -log(p) = 2215715.0 after pass:transform: ( -10.72, -8.29, -3.33, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.24, -7.19, 7.50, -1402.84) dfp_em_step_func: 017: -log(p) = 2202174.2 after pass:transform: ( -10.73, -8.29, -3.34, 4022.15) ( 1.97, -5.83pass 2 through quasi-newton minimization... fp = 2202172.250000, fret = 2202172.250000, ftol = 0.000000, EPS = 0.000000 , -3.48, 1227.15) ( 3.23, -7.19, 7.49, -1402.84) dfp_em_step_func: 018: -log(p) = 2202172.2 after pass:transform: ( -10.73, -8.29, -3.34, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.23, -7.19, 7.49, -1402.84) dfp_em_step_func: 019: -log(p) = 2202168.2 after pass:transform: ( -10.73, -8.29, -3.34, 4022.15) ( 1.97, -5.83, -3.48, 1227.15) ( 3.23, -7.19, 7.49, -1402.84) outof QuasiNewtonEMA: 021: -log(p) = 2202172.2 tol 0.000000 final transform: -10.726 -8.291 -3.339 4022.153; 1.969 -5.829 -3.480 1227.149; 3.232 -7.191 7.488 -1402.841; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 46 minutes and 22 seconds. #-------------------------------------- #@# SubCort Seg Tue Oct 16 23:54:59 CDT 2007 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca aseg.auto.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 /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca... setting gca type = Normal gca type reading input volume from norm.mgz... average std[0] = 7.4 reading transform from transforms/talairach.m3z... gcam->type = vox reading labels out of gcam file... Atlas used for the 3D morph was /pkg/brainmap/freesurfer-v3.0.5/average/RB_all_2006-02-15.gca average std = 7.4 using min determinant for regularization = 5.5 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13482 (104) mri peak = 0.17655 (110) gca peak = 0.19307 (105) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07702 (114) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.07016 (114) mri peak = 0.18989 (105) Left_Cerebral_White_Matter (2): linear fit = 0.93 x + 0.0 (2364 voxels, overlap=0.328) gca peak = 0.10443 (32) mri peak = 0.22940 (92) CSF peak too bright - rejecting gca peak = 0.11491 (25) mri peak = 0.14105 (111) CSF peak too bright - rejecting gca peak = 0.27319 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.29477 (66) mri peak = 0.09362 (90) Left_Hippocampus (17): linear fit = 1.52 x + 0.0 (51 voxels, overlap=0.000) gca peak = 0.06920 (68) mri peak = 0.07916 (112) unreasonable value (108.8), not in range [40, 95] - rejecting gca peak = 0.08287 (69) mri peak = 0.24071 (56) Right_Cerebral_Cortex (42): linear fit = 0.82 x + 0.0 (114 voxels, overlap=0.032) gca peak = 0.22476 (80) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.18589 (81) mri peak = 0.17232 (99) gca peak = 0.08091 (61) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.10638 (61) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15522 (88) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.12507 (87) mri peak = 0.20198 (94) gca peak = 0.25800 (69) mri peak = 0.13425 (109) gca peak = 0.29193 (67) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11200 (101) mri peak = 0.19814 (103) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (322 voxels, overlap=0.494) gca peak = 0.10010 (92) mri peak = 0.12243 (97) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (68 voxels, overlap=0.579) gca peak = 0.07167 (89) mri peak = 0.30499 (104) unreasonable value (111.2), not in range [60, 100] - rejecting gca peak = 0.09514 (89) mri peak = 0.18829 (103) gca peak = 0.07535 (89) mri peak = 0.17830 (95) Brain_Stem (16): linear fit = 1.10 x + 0.0 (548 voxels, overlap=0.238) gca peak = 0.11225 (101) mri peak = 0.15564 (102) gca peak = 0.15721 (97) mri peak = 0.19347 (102) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (143 voxels, overlap=0.526) gca peak = 0.13106 (39) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19587 (25) not using caudate to estimate GM means setting label Left_Cerebral_White_Matter based on Right_Cerebral_White_Matter = 0.93 x + 0 setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 0.82 x + 0 setting label Left_VentralDC based on Right_VentralDC = 1.05 x + 0 uniform distribution in MR - rejecting arbitrary fit estimating mean gm scale to be 0.82 x + 0.0 estimating mean wm scale to be 0.93 x + 0.0 estimating mean csf scale to be 1.00 x + 0.0 setting left cbm cortex = 0.82 x + 0.00 setting right cbm cortex = 0.82 x + 0.00 589 gm and wm labels changed (%17 to gray, %83 to white out of all changed labels) 6 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 5067 changed. pass 2: 946 changed. 400 border labels changed to MLE ... writing labeled volume to aseg.auto.mgz... auto-labeling took 39 minutes and 3 seconds. cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# ASeg Stats Wed Oct 17 00:34:04 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --ctab-default --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject 990903_61167 Using defalt ctab /pkg/brainmap/freesurfer-v3.0.5/FreeSurferColorLUT.txt atlas_icv = 2295.95 Loading mri/aseg.mgz Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 156167 # brainmaskvolume 156167.0 # nbrainsegvoxels 66613 # brainsegvolume 66613.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 686 segmentations Computing statistics for each segmentation 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter 37438 37438 3 3 Left-Cerebral-Cortex 2712 2712 4 4 Left-Lateral-Ventricle 105 105 5 5 Left-Inf-Lat-Vent 100 100 6 6 Left-Cerebellum-Exterior 0 7 7 Left-Cerebellum-White-Matter 726 726 8 8 Left-Cerebellum-Cortex 198 198 9 9 Left-Thalamus 0 10 10 Left-Thalamus-Proper 1302 1302 11 11 Left-Caudate 210 210 12 12 Left-Putamen 401 401 13 13 Left-Pallidum 227 227 14 14 3rd-Ventricle 5 5 15 15 4th-Ventricle 1 1 16 16 Brain-Stem 2126 2126 17 17 Left-Hippocampus 130 130 18 18 Left-Amygdala 23 23 19 19 Left-Insula 0 20 20 Left-Operculum 0 21 21 Line-1 0 22 22 Line-2 0 23 23 Line-3 0 24 24 CSF 8 8 25 25 Left-Lesion 0 26 26 Left-Accumbens-area 6 6 27 27 Left-Substancia-Nigra 0 28 28 Left-VentralDC 1149 1149 29 29 Left-undetermined 0 30 30 Left-vessel 10 10 31 31 Left-choroid-plexus 0 32 32 Left-F3orb 0 33 33 Left-lOg 0 34 34 Left-aOg 0 35 35 Left-mOg 0 36 36 Left-pOg 0 37 37 Left-Stellate 0 38 38 Left-Porg 0 39 39 Left-Aorg 0 40 40 Right-Cerebral-Exterior 0 41 41 Right-Cerebral-White-Matter 10094 10094 42 42 Right-Cerebral-Cortex 7999 7999 43 43 Right-Lateral-Ventricle 55 55 44 44 Right-Inf-Lat-Vent 3 3 45 45 Right-Cerebellum-Exterior 0 46 46 Right-Cerebellum-White-Matter 558 558 47 47 Right-Cerebellum-Cortex 106 106 48 48 Right-Thalamus 0 49 49 Right-Thalamus-Proper 505 505 50 50 Right-Caudate 109 109 51 51 Right-Putamen 98 98 52 52 Right-Pallidum 96 96 53 53 Right-Hippocampus 22 22 54 54 Right-Amygdala 6 6 55 55 Right-Insula 0 56 56 Right-Operculum 0 57 57 Right-Lesion 0 58 58 Right-Accumbens-area 7 7 59 59 Right-Substancia-Nigra 0 60 60 Right-VentralDC 404 404 61 61 Right-undetermined 0 62 62 Right-vessel 0 63 63 Right-choroid-plexus 0 64 64 Right-F3orb 0 65 65 Right-lOg 0 66 66 Right-aOg 0 67 67 Right-mOg 0 68 68 Right-pOg 0 69 69 Right-Stellate 0 70 70 Right-Porg 0 71 71 Right-Aorg 0 72 72 5th-Ventricle 1 1 73 73 Left-Interior 0 74 74 Right-Interior 0 75 75 Left-Lateral-Ventricles 0 76 76 Right-Lateral-Ventricles 0 77 77 WM-hypointensities 0 78 78 Left-WM-hypointensities 29 29 79 79 Right-WM-hypointensities 42 42 80 80 non-WM-hypointensities 0 81 81 Left-non-WM-hypointensities 3 3 82 82 Right-non-WM-hypointensities 0 83 83 Left-F1 0 84 84 Right-F1 0 85 85 Optic-Chiasm 189 189 86 86 Corpus_Callosum 0 87 96 Left-Amygdala-Anterior 0 88 97 Right-Amygdala-Anterior 0 89 98 Dura 0 90 100 Left-wm-intensity-abnormality 0 91 101 Left-caudate-intensity-abnormality 0 92 102 Left-putamen-intensity-abnormality 0 93 103 Left-accumbens-intensity-abnormality 0 94 104 Left-pallidum-intensity-abnormality 0 95 105 Left-amygdala-intensity-abnormality 0 96 106 Left-hippocampus-intensity-abnormality 0 97 107 Left-thalamus-intensity-abnormality 0 98 108 Left-VDC-intensity-abnormality 0 99 109 Right-wm-intensity-abnormality 0 100 110 Right-caudate-intensity-abnormality 0 101 111 Right-putamen-intensity-abnormality 0 102 112 Right-accumbens-intensity-abnormality 0 103 113 Right-pallidum-intensity-abnormality 0 104 114 Right-amygdala-intensity-abnormality 0 105 115 Right-hippocampus-intensity-abnormality 0 106 116 Right-thalamus-intensity-abnormality 0 107 117 Right-VDC-intensity-abnormality 0 108 118 Epidermis 0 109 119 Conn-Tissue 0 110 120 SC-Fat/Muscle 0 111 121 Cranium 0 112 122 CSF-SA 0 113 123 Muscle 0 114 124 Ear 0 115 125 Adipose 0 116 126 Spinal-Cord 0 117 127 Soft-Tissue 0 118 128 Nerve 0 119 129 Bone 0 120 130 Air 0 121 131 Orbital-Fat 0 122 132 Tongue 0 123 133 Nasal-Structures 0 124 134 Globe 0 125 135 Teeth 0 126 136 Left-Caudate/Putamen 0 127 137 Right-Caudate/Putamen 0 128 138 Left-Claustrum 0 129 139 Right-Claustrum 0 130 140 Cornea 0 131 142 Diploe 0 132 143 Vitreous-Humor 0 133 144 Lens 0 134 145 Aqueous-Humor 0 135 146 Outer-Table 0 136 147 Inner-Table 0 137 148 Periosteum 0 138 149 Endosteum 0 139 150 R/C/S 0 140 151 Iris 0 141 152 SC-Adipose/Muscle 0 142 153 SC-Tissue 0 143 154 Orbital-Adipose 0 144 193 Left-hippocampal_fissure 0 145 194 Left-CADG-head 0 146 195 Left-subiculum 0 147 196 Left-fimbria 0 148 197 Right-hippocampal_fissure 0 149 198 Right-CADG-head 0 150 199 Right-subiculum 0 151 200 Right-fimbria 0 152 201 alveus 0 153 202 perforant_pathway 0 154 203 parasubiculum 0 155 204 presubiculum 0 156 205 subiculum 0 157 206 CA1 0 158 207 CA2 0 159 208 CA3 0 160 209 CA4 0 161 210 GC-DG 0 162 211 HATA 0 163 212 fimbria 0 164 213 lateral_ventricle 0 165 214 molecular_layer_HP 0 166 215 hippocampal_fissure 0 167 216 entorhinal_cortex 0 168 217 molecular_layer_subiculum 0 169 218 Amygdala 0 170 219 Cerebral_White_Matter 0 171 220 Cerebral_Cortex 0 172 221 Inf_Lat_Vent 0 173 222 Ectorhinal 0 174 222 Perirhinal 0 175 223 Cerebral_White_Matter_Edge 0 176 224 fMRI_Background 0 177 331 Aorta 0 178 332 Left-Common-IliacA 0 179 333 Right-Common-IliacA 0 180 334 Left-External-IliacA 0 181 335 Right-External-IliacA 0 182 336 Left-Internal-IliacA 0 183 337 Right-Internal-IliacA 0 184 338 Left-Lateral-SacralA 0 185 339 Right-Lateral-SacralA 0 186 340 Left-ObturatorA 0 187 341 Right-ObturatorA 0 188 342 Left-Internal-PudendalA 0 189 343 Right-Internal-PudendalA 0 190 344 Left-UmbilicalA 0 191 345 Right-UmbilicalA 0 192 346 Left-Inf-RectalA 0 193 347 Right-Inf-RectalA 0 194 348 Left-Common-IliacV 0 195 349 Right-Common-IliacV 0 196 350 Left-External-IliacV 0 197 351 Right-External-IliacV 0 198 352 Left-Internal-IliacV 0 199 353 Right-Internal-IliacV 0 200 354 Left-ObturatorV 0 201 355 Right-ObturatorV 0 202 356 Left-Internal-PudendalV 0 203 357 Right-Internal-PudendalV 0 204 358 Pos-Lymph 0 205 359 Neg-Lymph 0 206 400 V1 0 207 401 V2 0 208 402 BA44 0 209 403 BA45 0 210 404 BA4a 0 211 405 BA4p 0 212 406 BA6 0 213 407 BA2 0 214 408 BAun1 0 215 409 BAun2 0 216 1000 ctx-lh-unknown 0 217 1001 ctx-lh-bankssts 0 218 1002 ctx-lh-caudalanteriorcingulate 0 219 1003 ctx-lh-caudalmiddlefrontal 0 220 1004 ctx-lh-corpuscallosum 0 221 1005 ctx-lh-cuneus 0 222 1006 ctx-lh-entorhinal 0 223 1007 ctx-lh-fusiform 0 224 1008 ctx-lh-inferiorparietal 0 225 1009 ctx-lh-inferiortemporal 0 226 1010 ctx-lh-isthmuscingulate 0 227 1011 ctx-lh-lateraloccipital 0 228 1012 ctx-lh-lateralorbitofrontal 0 229 1013 ctx-lh-lingual 0 230 1014 ctx-lh-medialorbitofrontal 0 231 1015 ctx-lh-middletemporal 0 232 1016 ctx-lh-parahippocampal 0 233 1017 ctx-lh-paracentral 0 234 1018 ctx-lh-parsopercularis 0 235 1019 ctx-lh-parsorbitalis 0 236 1020 ctx-lh-parstriangularis 0 237 1021 ctx-lh-pericalcarine 0 238 1022 ctx-lh-postcentral 0 239 1023 ctx-lh-posteriorcingulate 0 240 1024 ctx-lh-precentral 0 241 1025 ctx-lh-precuneus 0 242 1026 ctx-lh-rostralanteriorcingulate 0 243 1027 ctx-lh-rostralmiddlefrontal 0 244 1028 ctx-lh-superiorfrontal 0 245 1029 ctx-lh-superiorparietal 0 246 1030 ctx-lh-superiortemporal 0 247 1031 ctx-lh-supramarginal 0 248 1032 ctx-lh-frontalpole 0 249 1033 ctx-lh-temporalpole 0 250 1034 ctx-lh-transversetemporal 0 251 2000 ctx-rh-unknown 0 252 2001 ctx-rh-bankssts 0 253 2002 ctx-rh-caudalanteriorcingulate 0 254 2003 ctx-rh-caudalmiddlefrontal 0 255 2004 ctx-rh-corpuscallosum 0 256 2005 ctx-rh-cuneus 0 257 2006 ctx-rh-entorhinal 0 258 2007 ctx-rh-fusiform 0 259 2008 ctx-rh-inferiorparietal 0 260 2009 ctx-rh-inferiortemporal 0 261 2010 ctx-rh-isthmuscingulate 0 262 2011 ctx-rh-lateraloccipital 0 263 2012 ctx-rh-lateralorbitofrontal 0 264 2013 ctx-rh-lingual 0 265 2014 ctx-rh-medialorbitofrontal 0 266 2015 ctx-rh-middletemporal 0 267 2016 ctx-rh-parahippocampal 0 268 2017 ctx-rh-paracentral 0 269 2018 ctx-rh-parsopercularis 0 270 2019 ctx-rh-parsorbitalis 0 271 2020 ctx-rh-parstriangularis 0 272 2021 ctx-rh-pericalcarine 0 273 2022 ctx-rh-postcentral 0 274 2023 ctx-rh-posteriorcingulate 0 275 2024 ctx-rh-precentral 0 276 2025 ctx-rh-precuneus 0 277 2026 ctx-rh-rostralanteriorcingulate 0 278 2027 ctx-rh-rostralmiddlefrontal 0 279 2028 ctx-rh-superiorfrontal 0 280 2029 ctx-rh-superiorparietal 0 281 2030 ctx-rh-superiortemporal 0 282 2031 ctx-rh-supramarginal 0 283 2032 ctx-rh-frontalpole 0 284 2033 ctx-rh-temporalpole 0 285 2034 ctx-rh-transversetemporal 0 286 3000 wm-lh-unknown 0 287 3001 wm-lh-bankssts 0 288 3002 wm-lh-caudalanteriorcingulate 0 289 3003 wm-lh-caudalmiddlefrontal 0 290 3004 wm-lh-corpuscallosum 0 291 3005 wm-lh-cuneus 0 292 3006 wm-lh-entorhinal 0 293 3007 wm-lh-fusiform 0 294 3008 wm-lh-inferiorparietal 0 295 3009 wm-lh-inferiortemporal 0 296 3010 wm-lh-isthmuscingulate 0 297 3011 wm-lh-lateraloccipital 0 298 3012 wm-lh-lateralorbitofrontal 0 299 3013 wm-lh-lingual 0 300 3014 wm-lh-medialorbitofrontal 0 301 3015 wm-lh-middletemporal 0 302 3016 wm-lh-parahippocampal 0 303 3017 wm-lh-paracentral 0 304 3018 wm-lh-parsopercularis 0 305 3019 wm-lh-parsorbitalis 0 306 3020 wm-lh-parstriangularis 0 307 3021 wm-lh-pericalcarine 0 308 3022 wm-lh-postcentral 0 309 3023 wm-lh-posteriorcingulate 0 310 3024 wm-lh-precentral 0 311 3025 wm-lh-precuneus 0 312 3026 wm-lh-rostralanteriorcingulate 0 313 3027 wm-lh-rostralmiddlefrontal 0 314 3028 wm-lh-superiorfrontal 0 315 3029 wm-lh-superiorparietal 0 316 3030 wm-lh-superiortemporal 0 317 3031 wm-lh-supramarginal 0 318 3032 wm-lh-frontalpole 0 319 3033 wm-lh-temporalpole 0 320 3034 wm-lh-transversetemporal 0 321 4000 wm-rh-unknown 0 322 4001 wm-rh-bankssts 0 323 4002 wm-rh-caudalanteriorcingulate 0 324 4003 wm-rh-caudalmiddlefrontal 0 325 4004 wm-rh-corpuscallosum 0 326 4005 wm-rh-cuneus 0 327 4006 wm-rh-entorhinal 0 328 4007 wm-rh-fusiform 0 329 4008 wm-rh-inferiorparietal 0 330 4009 wm-rh-inferiortemporal 0 331 4010 wm-rh-isthmuscingulate 0 332 4011 wm-rh-lateraloccipital 0 333 4012 wm-rh-lateralorbitofrontal 0 334 4013 wm-rh-lingual 0 335 4014 wm-rh-medialorbitofrontal 0 336 4015 wm-rh-middletemporal 0 337 4016 wm-rh-parahippocampal 0 338 4017 wm-rh-paracentral 0 339 4018 wm-rh-parsopercularis 0 340 4019 wm-rh-parsorbitalis 0 341 4020 wm-rh-parstriangularis 0 342 4021 wm-rh-pericalcarine 0 343 4022 wm-rh-postcentral 0 344 4023 wm-rh-posteriorcingulate 0 345 4024 wm-rh-precentral 0 346 4025 wm-rh-precuneus 0 347 4026 wm-rh-rostralanteriorcingulate 0 348 4027 wm-rh-rostralmiddlefrontal 0 349 4028 wm-rh-superiorfrontal 0 350 4029 wm-rh-superiorparietal 0 351 4030 wm-rh-superiortemporal 0 352 4031 wm-rh-supramarginal 0 353 4032 wm-rh-frontalpole 0 354 4033 wm-rh-temporalpole 0 355 4034 wm-rh-transversetemporal 0 356 5001 wm-lh-centrum-semiovale 0 357 5002 wm-rh-centrum-semiovale 0 358 1100 ctx-lh-Unknown 0 359 1101 ctx-lh-Corpus_callosum 0 360 1102 ctx-lh-G_and_S_Insula_ONLY_AVERAGE 0 361 1103 ctx-lh-G_cingulate-Isthmus 0 362 1104 ctx-lh-G_cingulate-Main_part 0 363 1105 ctx-lh-G_cuneus 0 364 1106 ctx-lh-G_frontal_inf-Opercular_part 0 365 1107 ctx-lh-G_frontal_inf-Orbital_part 0 366 1108 ctx-lh-G_frontal_inf-Triangular_part 0 367 1109 ctx-lh-G_frontal_middle 0 368 1110 ctx-lh-G_frontal_superior 0 369 1111 ctx-lh-G_frontomarginal 0 370 1112 ctx-lh-G_insular_long 0 371 1113 ctx-lh-G_insular_short 0 372 1114 ctx-lh-G_and_S_occipital_inferior 0 373 1115 ctx-lh-G_occipital_middle 0 374 1116 ctx-lh-G_occipital_superior 0 375 1117 ctx-lh-G_occipit-temp_lat-Or_fusiform 0 376 1118 ctx-lh-G_occipit-temp_med-Lingual_part 0 377 1119 ctx-lh-G_occipit-temp_med-Parahippocampal_part 0 378 1120 ctx-lh-G_orbital 0 379 1121 ctx-lh-G_paracentral 0 380 1122 ctx-lh-G_parietal_inferior-Angular_part 0 381 1123 ctx-lh-G_parietal_inferior-Supramarginal_part 0 382 1124 ctx-lh-G_parietal_superior 0 383 1125 ctx-lh-G_postcentral 0 384 1126 ctx-lh-G_precentral 0 385 1127 ctx-lh-G_precuneus 0 386 1128 ctx-lh-G_rectus 0 387 1129 ctx-lh-G_subcallosal 0 388 1130 ctx-lh-G_subcentral 0 389 1131 ctx-lh-G_temporal_inferior 0 390 1132 ctx-lh-G_temporal_middle 0 391 1133 ctx-lh-G_temp_sup-G_temp_transv_and_interm_S 0 392 1134 ctx-lh-G_temp_sup-Lateral_aspect 0 393 1135 ctx-lh-G_temp_sup-Planum_polare 0 394 1136 ctx-lh-G_temp_sup-Planum_tempolare 0 395 1137 ctx-lh-G_and_S_transverse_frontopolar 0 396 1138 ctx-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 397 1139 ctx-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 398 1140 ctx-lh-Lat_Fissure-post_sgt 0 399 1141 ctx-lh-Medial_wall 0 400 1142 ctx-lh-Pole_occipital 0 401 1143 ctx-lh-Pole_temporal 0 402 1144 ctx-lh-S_calcarine 0 403 1145 ctx-lh-S_central 0 404 1146 ctx-lh-S_central_insula 0 405 1147 ctx-lh-S_cingulate-Main_part_and_Intracingulate 0 406 1148 ctx-lh-S_cingulate-Marginalis_part 0 407 1149 ctx-lh-S_circular_insula_anterior 0 408 1150 ctx-lh-S_circular_insula_inferior 0 409 1151 ctx-lh-S_circular_insula_superior 0 410 1152 ctx-lh-S_collateral_transverse_ant 0 411 1153 ctx-lh-S_collateral_transverse_post 0 412 1154 ctx-lh-S_frontal_inferior 0 413 1155 ctx-lh-S_frontal_middle 0 414 1156 ctx-lh-S_frontal_superior 0 415 1157 ctx-lh-S_frontomarginal 0 416 1158 ctx-lh-S_intermedius_primus-Jensen 0 417 1159 ctx-lh-S_intraparietal-and_Parietal_transverse 0 418 1160 ctx-lh-S_occipital_anterior 0 419 1161 ctx-lh-S_occipital_middle_and_Lunatus 0 420 1162 ctx-lh-S_occipital_superior_and_transversalis 0 421 1163 ctx-lh-S_occipito-temporal_lateral 0 422 1164 ctx-lh-S_occipito-temporal_medial_and_S_Lingual 0 423 1165 ctx-lh-S_orbital-H_shapped 0 424 1166 ctx-lh-S_orbital_lateral 0 425 1167 ctx-lh-S_orbital_medial-Or_olfactory 0 426 1168 ctx-lh-S_paracentral 0 427 1169 ctx-lh-S_parieto_occipital 0 428 1170 ctx-lh-S_pericallosal 0 429 1171 ctx-lh-S_postcentral 0 430 1172 ctx-lh-S_precentral-Inferior-part 0 431 1173 ctx-lh-S_precentral-Superior-part 0 432 1174 ctx-lh-S_subcentral_ant 0 433 1175 ctx-lh-S_subcentral_post 0 434 1176 ctx-lh-S_suborbital 0 435 1177 ctx-lh-S_subparietal 0 436 1178 ctx-lh-S_supracingulate 0 437 1179 ctx-lh-S_temporal_inferior 0 438 1180 ctx-lh-S_temporal_superior 0 439 1181 ctx-lh-S_temporal_transverse 0 440 2100 ctx-rh-Unknown 0 441 2101 ctx-rh-Corpus_callosum 0 442 2102 ctx-rh-G_and_S_Insula_ONLY_AVERAGE 0 443 2103 ctx-rh-G_cingulate-Isthmus 0 444 2104 ctx-rh-G_cingulate-Main_part 0 445 2105 ctx-rh-G_cuneus 0 446 2106 ctx-rh-G_frontal_inf-Opercular_part 0 447 2107 ctx-rh-G_frontal_inf-Orbital_part 0 448 2108 ctx-rh-G_frontal_inf-Triangular_part 0 449 2109 ctx-rh-G_frontal_middle 0 450 2110 ctx-rh-G_frontal_superior 0 451 2111 ctx-rh-G_frontomarginal 0 452 2112 ctx-rh-G_insular_long 0 453 2113 ctx-rh-G_insular_short 0 454 2114 ctx-rh-G_and_S_occipital_inferior 0 455 2115 ctx-rh-G_occipital_middle 0 456 2116 ctx-rh-G_occipital_superior 0 457 2117 ctx-rh-G_occipit-temp_lat-Or_fusiform 0 458 2118 ctx-rh-G_occipit-temp_med-Lingual_part 0 459 2119 ctx-rh-G_occipit-temp_med-Parahippocampal_part 0 460 2120 ctx-rh-G_orbital 0 461 2121 ctx-rh-G_paracentral 0 462 2122 ctx-rh-G_parietal_inferior-Angular_part 0 463 2123 ctx-rh-G_parietal_inferior-Supramarginal_part 0 464 2124 ctx-rh-G_parietal_superior 0 465 2125 ctx-rh-G_postcentral 0 466 2126 ctx-rh-G_precentral 0 467 2127 ctx-rh-G_precuneus 0 468 2128 ctx-rh-G_rectus 0 469 2129 ctx-rh-G_subcallosal 0 470 2130 ctx-rh-G_subcentral 0 471 2131 ctx-rh-G_temporal_inferior 0 472 2132 ctx-rh-G_temporal_middle 0 473 2133 ctx-rh-G_temp_sup-G_temp_transv_and_interm_S 0 474 2134 ctx-rh-G_temp_sup-Lateral_aspect 0 475 2135 ctx-rh-G_temp_sup-Planum_polare 0 476 2136 ctx-rh-G_temp_sup-Planum_tempolare 0 477 2137 ctx-rh-G_and_S_transverse_frontopolar 0 478 2138 ctx-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 479 2139 ctx-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 480 2140 ctx-rh-Lat_Fissure-post_sgt 0 481 2141 ctx-rh-Medial_wall 0 482 2142 ctx-rh-Pole_occipital 0 483 2143 ctx-rh-Pole_temporal 0 484 2144 ctx-rh-S_calcarine 0 485 2145 ctx-rh-S_central 0 486 2146 ctx-rh-S_central_insula 0 487 2147 ctx-rh-S_cingulate-Main_part_and_Intracingulate 0 488 2148 ctx-rh-S_cingulate-Marginalis_part 0 489 2149 ctx-rh-S_circular_insula_anterior 0 490 2150 ctx-rh-S_circular_insula_inferior 0 491 2151 ctx-rh-S_circular_insula_superior 0 492 2152 ctx-rh-S_collateral_transverse_ant 0 493 2153 ctx-rh-S_collateral_transverse_post 0 494 2154 ctx-rh-S_frontal_inferior 0 495 2155 ctx-rh-S_frontal_middle 0 496 2156 ctx-rh-S_frontal_superior 0 497 2157 ctx-rh-S_frontomarginal 0 498 2158 ctx-rh-S_intermedius_primus-Jensen 0 499 2159 ctx-rh-S_intraparietal-and_Parietal_transverse 0 500 2160 ctx-rh-S_occipital_anterior 0 501 2161 ctx-rh-S_occipital_middle_and_Lunatus 0 502 2162 ctx-rh-S_occipital_superior_and_transversalis 0 503 2163 ctx-rh-S_occipito-temporal_lateral 0 504 2164 ctx-rh-S_occipito-temporal_medial_and_S_Lingual 0 505 2165 ctx-rh-S_orbital-H_shapped 0 506 2166 ctx-rh-S_orbital_lateral 0 507 2167 ctx-rh-S_orbital_medial-Or_olfactory 0 508 2168 ctx-rh-S_paracentral 0 509 2169 ctx-rh-S_parieto_occipital 0 510 2170 ctx-rh-S_pericallosal 0 511 2171 ctx-rh-S_postcentral 0 512 2172 ctx-rh-S_precentral-Inferior-part 0 513 2173 ctx-rh-S_precentral-Superior-part 0 514 2174 ctx-rh-S_subcentral_ant 0 515 2175 ctx-rh-S_subcentral_post 0 516 2176 ctx-rh-S_suborbital 0 517 2177 ctx-rh-S_subparietal 0 518 2178 ctx-rh-S_supracingulate 0 519 2179 ctx-rh-S_temporal_inferior 0 520 2180 ctx-rh-S_temporal_superior 0 521 2181 ctx-rh-S_temporal_transverse 0 522 3100 wm-lh-Unknown 0 523 3101 wm-lh-Corpus_callosum 0 524 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 525 3103 wm-lh-G_cingulate-Isthmus 0 526 3104 wm-lh-G_cingulate-Main_part 0 527 3105 wm-lh-G_cuneus 0 528 3106 wm-lh-G_frontal_inf-Opercular_part 0 529 3107 wm-lh-G_frontal_inf-Orbital_part 0 530 3108 wm-lh-G_frontal_inf-Triangular_part 0 531 3109 wm-lh-G_frontal_middle 0 532 3110 wm-lh-G_frontal_superior 0 533 3111 wm-lh-G_frontomarginal 0 534 3112 wm-lh-G_insular_long 0 535 3113 wm-lh-G_insular_short 0 536 3114 wm-lh-G_and_S_occipital_inferior 0 537 3115 wm-lh-G_occipital_middle 0 538 3116 wm-lh-G_occipital_superior 0 539 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 540 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 541 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 542 3120 wm-lh-G_orbital 0 543 3121 wm-lh-G_paracentral 0 544 3122 wm-lh-G_parietal_inferior-Angular_part 0 545 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 546 3124 wm-lh-G_parietal_superior 0 547 3125 wm-lh-G_postcentral 0 548 3126 wm-lh-G_precentral 0 549 3127 wm-lh-G_precuneus 0 550 3128 wm-lh-G_rectus 0 551 3129 wm-lh-G_subcallosal 0 552 3130 wm-lh-G_subcentral 0 553 3131 wm-lh-G_temporal_inferior 0 554 3132 wm-lh-G_temporal_middle 0 555 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 556 3134 wm-lh-G_temp_sup-Lateral_aspect 0 557 3135 wm-lh-G_temp_sup-Planum_polare 0 558 3136 wm-lh-G_temp_sup-Planum_tempolare 0 559 3137 wm-lh-G_and_S_transverse_frontopolar 0 560 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 561 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 562 3140 wm-lh-Lat_Fissure-post_sgt 0 563 3141 wm-lh-Medial_wall 0 564 3142 wm-lh-Pole_occipital 0 565 3143 wm-lh-Pole_temporal 0 566 3144 wm-lh-S_calcarine 0 567 3145 wm-lh-S_central 0 568 3146 wm-lh-S_central_insula 0 569 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 570 3148 wm-lh-S_cingulate-Marginalis_part 0 571 3149 wm-lh-S_circular_insula_anterior 0 572 3150 wm-lh-S_circular_insula_inferior 0 573 3151 wm-lh-S_circular_insula_superior 0 574 3152 wm-lh-S_collateral_transverse_ant 0 575 3153 wm-lh-S_collateral_transverse_post 0 576 3154 wm-lh-S_frontal_inferior 0 577 3155 wm-lh-S_frontal_middle 0 578 3156 wm-lh-S_frontal_superior 0 579 3157 wm-lh-S_frontomarginal 0 580 3158 wm-lh-S_intermedius_primus-Jensen 0 581 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 582 3160 wm-lh-S_occipital_anterior 0 583 3161 wm-lh-S_occipital_middle_and_Lunatus 0 584 3162 wm-lh-S_occipital_superior_and_transversalis 0 585 3163 wm-lh-S_occipito-temporal_lateral 0 586 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 587 3165 wm-lh-S_orbital-H_shapped 0 588 3166 wm-lh-S_orbital_lateral 0 589 3167 wm-lh-S_orbital_medial-Or_olfactory 0 590 3168 wm-lh-S_paracentral 0 591 3169 wm-lh-S_parieto_occipital 0 592 3170 wm-lh-S_pericallosal 0 593 3171 wm-lh-S_postcentral 0 594 3172 wm-lh-S_precentral-Inferior-part 0 595 3173 wm-lh-S_precentral-Superior-part 0 596 3174 wm-lh-S_subcentral_ant 0 597 3175 wm-lh-S_subcentral_post 0 598 3176 wm-lh-S_suborbital 0 599 3177 wm-lh-S_subparietal 0 600 3178 wm-lh-S_supracingulate 0 601 3179 wm-lh-S_temporal_inferior 0 602 3180 wm-lh-S_temporal_superior 0 603 3181 wm-lh-S_temporal_transverse 0 604 4100 wm-rh-Unknown 0 605 4101 wm-rh-Corpus_callosum 0 606 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 607 4103 wm-rh-G_cingulate-Isthmus 0 608 4104 wm-rh-G_cingulate-Main_part 0 609 4105 wm-rh-G_cuneus 0 610 4106 wm-rh-G_frontal_inf-Opercular_part 0 611 4107 wm-rh-G_frontal_inf-Orbital_part 0 612 4108 wm-rh-G_frontal_inf-Triangular_part 0 613 4109 wm-rh-G_frontal_middle 0 614 4110 wm-rh-G_frontal_superior 0 615 4111 wm-rh-G_frontomarginal 0 616 4112 wm-rh-G_insular_long 0 617 4113 wm-rh-G_insular_short 0 618 4114 wm-rh-G_and_S_occipital_inferior 0 619 4115 wm-rh-G_occipital_middle 0 620 4116 wm-rh-G_occipital_superior 0 621 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 622 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 623 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 624 4120 wm-rh-G_orbital 0 625 4121 wm-rh-G_paracentral 0 626 4122 wm-rh-G_parietal_inferior-Angular_part 0 627 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 628 4124 wm-rh-G_parietal_superior 0 629 4125 wm-rh-G_postcentral 0 630 4126 wm-rh-G_precentral 0 631 4127 wm-rh-G_precuneus 0 632 4128 wm-rh-G_rectus 0 633 4129 wm-rh-G_subcallosal 0 634 4130 wm-rh-G_subcentral 0 635 4131 wm-rh-G_temporal_inferior 0 636 4132 wm-rh-G_temporal_middle 0 637 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 638 4134 wm-rh-G_temp_sup-Lateral_aspect 0 639 4135 wm-rh-G_temp_sup-Planum_polare 0 640 4136 wm-rh-G_temp_sup-Planum_tempolare 0 641 4137 wm-rh-G_and_S_transverse_frontopolar 0 642 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 643 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 644 4140 wm-rh-Lat_Fissure-post_sgt 0 645 4141 wm-rh-Medial_wall 0 646 4142 wm-rh-Pole_occipital 0 647 4143 wm-rh-Pole_temporal 0 648 4144 wm-rh-S_calcarine 0 649 4145 wm-rh-S_central 0 650 4146 wm-rh-S_central_insula 0 651 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 652 4148 wm-rh-S_cingulate-Marginalis_part 0 653 4149 wm-rh-S_circular_insula_anterior 0 654 4150 wm-rh-S_circular_insula_inferior 0 655 4151 wm-rh-S_circular_insula_superior 0 656 4152 wm-rh-S_collateral_transverse_ant 0 657 4153 wm-rh-S_collateral_transverse_post 0 658 4154 wm-rh-S_frontal_inferior 0 659 4155 wm-rh-S_frontal_middle 0 660 4156 wm-rh-S_frontal_superior 0 661 4157 wm-rh-S_frontomarginal 0 662 4158 wm-rh-S_intermedius_primus-Jensen 0 663 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 664 4160 wm-rh-S_occipital_anterior 0 665 4161 wm-rh-S_occipital_middle_and_Lunatus 0 666 4162 wm-rh-S_occipital_superior_and_transversalis 0 667 4163 wm-rh-S_occipito-temporal_lateral 0 668 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 669 4165 wm-rh-S_orbital-H_shapped 0 670 4166 wm-rh-S_orbital_lateral 0 671 4167 wm-rh-S_orbital_medial-Or_olfactory 0 672 4168 wm-rh-S_paracentral 0 673 4169 wm-rh-S_parieto_occipital 0 674 4170 wm-rh-S_pericallosal 0 675 4171 wm-rh-S_postcentral 0 676 4172 wm-rh-S_precentral-Inferior-part 0 677 4173 wm-rh-S_precentral-Superior-part 0 678 4174 wm-rh-S_subcentral_ant 0 679 4175 wm-rh-S_subcentral_post 0 680 4176 wm-rh-S_suborbital 0 681 4177 wm-rh-S_subparietal 0 682 4178 wm-rh-S_supracingulate 0 683 4179 wm-rh-S_temporal_inferior 0 684 4180 wm-rh-S_temporal_superior 0 685 4181 wm-rh-S_temporal_transverse 0 Reporting on 685 segmentations #-------------------------------------------- #@# Intensity Normalization2 Wed Oct 17 00:46:37 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_normalize -mask brainmask.mgz -aseg aseg.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 25891 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 6 minutes and 40 seconds. using MR volume brainmask.mgz to mask input volume... using wm threshold 94.0 for removing exterior voxels white matter peak found at 99 gm peak at 50 (50), valley at 39 (39) csf peak at 18, setting threshold to 39 white matter peak found at 110 gm peak at 76 (76), valley at 0 (-1) csf peak at 38, setting threshold to 63 #-------------------------------------------- #@# Mask BFS Wed Oct 17 00:53:27 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 writing masked volume to brain.finalsurfs.mgz... #-------------------------------------------- #@# WM Segmentation Wed Oct 17 00:53:36 CDT 2007 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: 108.8 +- 5.7 [95.0 --> 125.0] GM: 70.7 +- 6.0 [46.0 --> 96.0] setting bottom of white matter range to 76.7 setting top of gray matter range to 82.7 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... 73 sparsely connected voxels removed... thickening thin strands.... 20 segments, 122 filled 3 bright non-wm voxels segmented. 177 diagonally connected voxels added... white matter segmentation took 3.0 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 0.81 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 8 additional wm voxels added 0 additional wm voxels added SEG EDIT: 189 voxels turned on, 37885 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+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 3 found - 3 modified | TOTAL: 5 pass 2 (xy-): 0 found - 3 modified | TOTAL: 5 pass 1 (yz+): 4 found - 4 modified | TOTAL: 9 pass 2 (yz+): 0 found - 4 modified | TOTAL: 9 pass 1 (yz-): 6 found - 6 modified | TOTAL: 15 pass 2 (yz-): 0 found - 6 modified | TOTAL: 15 pass 1 (xz+): 2 found - 2 modified | TOTAL: 17 pass 2 (xz+): 0 found - 2 modified | TOTAL: 17 pass 1 (xz-): 4 found - 4 modified | TOTAL: 21 pass 2 (xz-): 0 found - 4 modified | TOTAL: 21 Iteration Number : 1 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 : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 3 found - 3 modified | TOTAL: 10 pass 2 (+-): 0 found - 3 modified | TOTAL: 10 pass 1 (--): 7 found - 7 modified | TOTAL: 17 pass 2 (--): 0 found - 7 modified | TOTAL: 17 pass 1 (-+): 4 found - 4 modified | TOTAL: 21 pass 2 (-+): 0 found - 4 modified | TOTAL: 21 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 1 found - 1 modified | TOTAL: 3 pass 2 (xy-): 0 found - 1 modified | TOTAL: 3 pass 1 (yz+): 0 found - 0 modified | TOTAL: 3 pass 1 (yz-): 0 found - 0 modified | TOTAL: 3 pass 1 (xz+): 0 found - 0 modified | TOTAL: 3 pass 1 (xz-): 0 found - 0 modified | TOTAL: 3 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 = 47 (out of 68141: 0.068975) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed Oct 17 00:57:39 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.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.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform -2.041 1.633 -1.480 652.893; 0.656 -1.924 -2.725 808.185; -1.921 -1.822 0.657 506.376; 0.000 0.000 0.000 1.000; Looking for area (min, max) = (350, 1400) area[0] = 17444 (min = 350, max = 1400), aspect = 0.81 (min = 0.10, max = 0.75) need search nearby using seed (113, 96, 30), TAL = (15.0, -98.0, 32.0) talairach voxel to voxel transform -0.224 0.058 -0.263 232.040; 0.173 -0.151 -0.235 127.831; -0.176 -0.247 0.103 262.158; 0.000 0.000 0.000 1.000; done. writing output to filled.mgz... filling took 2.3 minutes INFO: Modifying dst c_(r,a,s), using the transform dst INFO: Modifying dst c_(r,a,s), using the transform dst reading segmented volume aseg.mgz... INFO: Modifying dst c_(r,a,s), using the transform dst segmentation indicates cc at (113, 96, 30) --> (15.0, -98.0, 32.0) INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (15.00, -98.00, 32.00) ERASING BRAINSTEMseed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(33.00, -98.00, 32.00) SRC: (208.49, 122.75, 224.85) search lh wm seed point around talairach space (-3.00, -98.00, 32.00), SRC: (200.42, 128.97, 218.52) 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 Oct 17 00:59:59 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mri_tessellate ../mri/filled.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ slice 200: 624 vertices, 696 faces slice 210: 3798 vertices, 3919 faces slice 220: 7079 vertices, 7205 faces slice 230: 10413 vertices, 10555 faces slice 240: 14782 vertices, 14893 faces slice 250: 14999 vertices, 15018 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using ras2vox 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; #-------------------------------------------- #@# Smooth1 lh Wed Oct 17 01:02:46 CDT 2007 mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Wed Oct 17 01:02:47 CDT 2007 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts avg radius = 24.5 mm, total surface area = 9036 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.1 minutes Not saving sulc step 000: RMS=0.126 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.072 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.063 (target=0.015) step 025: RMS=0.058 (target=0.015) step 030: RMS=0.055 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.050 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.049 (target=0.015) step 060: RMS=0.048 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed Oct 17 01:02:56 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, host=vader, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90 surface projected - minimizing metric distortion... vertex spacing 2.79 +- 1.05 (0.02-->8.18) (max @ vno 2879 --> 2543) face area 0.30 +- 0.21 (-0.37-->2.09) tol=1.0e-01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 301: dt: 1850.70, sse: 82.8 (0.128, 10.8, 0.723), neg: 104 (%0.019:%0.11), avgs: 32 302: dt: 310.00, sse: 80.0 (0.124, 9.2, 0.721), neg: 69 (%0.012:%0.03), avgs: 32 303: dt: 611.90, sse: 79.2 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 304: dt: 0.29, sse: 79.2 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 305: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 306: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 307: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 308: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 309: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 310: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 vertex spacing 2.83 +- 1.01 (0.04-->8.25) (max @ vno 2543 --> 2542) face area 0.30 +- 0.21 (-0.09-->2.10) 311: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 312: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 313: dt: 0.29, sse: 79.3 (0.121, 8.5, 0.720), neg: 65 (%0.013:%0.03), avgs: 32 314: dt: 3052.08, sse: 77.5 (0.121, 9.7, 0.723), neg: 66 (%0.013:%0.03), avgs: 32 vertex spacing 2.84 +- 1.00 (0.03-->8.79) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.09-->2.11) 315: dt: 334.97, sse: 75.2 (0.122, 10.6, 0.724), neg: 83 (%0.016:%0.03), avgs: 8 316: dt: 45.28, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 317: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 318: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 319: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 320: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 vertex spacing 2.85 +- 0.99 (0.02-->8.65) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.09-->2.11) 321: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 322: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 323: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 324: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 325: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 326: dt: 0.15, sse: 74.4 (0.122, 10.3, 0.724), neg: 74 (%0.009:%0.02), avgs: 8 327: dt: 113.39, sse: 74.0 (0.122, 10.1, 0.724), neg: 73 (%0.010:%0.02), avgs: 8 vertex spacing 2.85 +- 0.99 (0.07-->8.66) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.13-->2.12) 328: dt: 3.10, sse: 73.8 (0.122, 10.1, 0.724), neg: 71 (%0.008:%0.02), avgs: 2 329: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 71 (%0.008:%0.02), avgs: 2 330: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 71 (%0.008:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.07-->8.66) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.08-->2.12) 331: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 71 (%0.008:%0.02), avgs: 2 332: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 70 (%0.008:%0.02), avgs: 2 333: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 70 (%0.008:%0.02), avgs: 2 334: dt: 0.09, sse: 73.8 (0.122, 10.1, 0.724), neg: 70 (%0.008:%0.02), avgs: 2 335: dt: 0.09, sse: 73.7 (0.122, 10.1, 0.724), neg: 71 (%0.008:%0.02), avgs: 2 336: dt: 0.09, sse: 73.7 (0.122, 10.1, 0.724), neg: 73 (%0.007:%0.02), avgs: 2 337: dt: 0.09, sse: 73.7 (0.122, 10.1, 0.724), neg: 72 (%0.007:%0.02), avgs: 2 338: dt: 0.09, sse: 73.7 (0.122, 10.1, 0.724), neg: 72 (%0.007:%0.02), avgs: 2 339: dt: 26.76, sse: 73.3 (0.123, 10.3, 0.724), neg: 81 (%0.011:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.07-->8.68) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.16-->2.13) 340: dt: 0.63, sse: 72.9 (0.123, 10.3, 0.724), neg: 79 (%0.007:%0.02), avgs: 0 vertex spacing 2.85 +- 0.99 (0.07-->8.69) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.07-->2.13) vertex spacing 2.85 +- 0.99 (0.07-->8.69) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.07-->2.13) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 341: dt: 489.71, sse: 4.8 (0.123, 10.3, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 342: dt: 0.29, sse: 4.8 (0.123, 10.3, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 343: dt: 0.29, sse: 4.8 (0.123, 10.3, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 344: dt: 0.29, sse: 4.8 (0.123, 10.3, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 345: dt: 0.29, sse: 4.8 (0.123, 10.3, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 346: dt: 0.29, sse: 4.8 (0.123, 10.4, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 347: dt: 0.29, sse: 4.9 (0.123, 10.4, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 348: dt: 0.29, sse: 4.9 (0.123, 10.4, 0.724), neg: 80 (%0.007:%0.02), avgs: 32 349: dt: 0.29, sse: 4.9 (0.123, 10.4, 0.724), neg: 78 (%0.007:%0.02), avgs: 32 350: dt: 0.29, sse: 4.9 (0.123, 10.4, 0.724), neg: 78 (%0.007:%0.02), avgs: 32 vertex spacing 2.85 +- 0.99 (0.05-->8.76) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.07-->2.14) 351: dt: 0.29, sse: 4.9 (0.123, 10.4, 0.724), neg: 78 (%0.007:%0.02), avgs: 32 352: dt: 488.30, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.007:%0.02), avgs: 32 vertex spacing 2.85 +- 0.99 (0.04-->8.82) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.06-->2.14) 353: dt: 20.98, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 354: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 355: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 356: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 79 (%0.006:%0.02), avgs: 8 357: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 77 (%0.006:%0.02), avgs: 8 358: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 77 (%0.006:%0.02), avgs: 8 359: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 77 (%0.006:%0.02), avgs: 8 360: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 vertex spacing 2.85 +- 0.99 (0.03-->8.83) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.05-->2.14) 361: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 362: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 363: dt: 0.15, sse: 4.8 (0.123, 10.5, 0.725), neg: 78 (%0.006:%0.02), avgs: 8 364: dt: 86.29, sse: 4.7 (0.123, 10.5, 0.725), neg: 77 (%0.005:%0.02), avgs: 8 vertex spacing 2.85 +- 0.99 (0.06-->8.85) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.04-->2.14) inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=172.575, avgs=0 005: dt: 0.9000, rms radial error=172.322, avgs=0 010: dt: 0.9000, rms radial error=171.777, avgs=0 015: dt: 0.9000, rms radial error=171.062, avgs=0 020: dt: 0.9000, rms radial error=170.246, avgs=0 025: dt: 0.9000, rms radial error=169.373, avgs=0 030: dt: 0.9000, rms radial error=168.468, avgs=0 035: dt: 0.9000, rms radial error=167.546, avgs=0 040: dt: 0.9000, rms radial error=166.616, avgs=0 045: dt: 0.9000, rms radial error=165.682, avgs=0 050: dt: 0.9000, rms radial error=164.748, avgs=0 055: dt: 0.9000, rms radial error=163.817, avgs=0 060: dt: 0.9000, rms radial error=162.889, avgs=0 065: dt: 0.9000, rms radial error=161.966, avgs=0 070: dt: 0.9000, rms radial error=161.047, avgs=0 075: dt: 0.9000, rms radial error=160.134, avgs=0 080: dt: 0.9000, rms radial error=159.225, avgs=0 085: dt: 0.9000, rms radial error=158.321, avgs=0 090: dt: 0.9000, rms radial error=157.422, avgs=0 095: dt: 0.9000, rms radial error=156.529, avgs=0 100: dt: 0.9000, rms radial error=155.640, avgs=0 105: dt: 0.9000, rms radial error=154.757, avgs=0 110: dt: 0.9000, rms radial error=153.878, avgs=0 115: dt: 0.9000, rms radial error=153.005, avgs=0 120: dt: 0.9000, rms radial error=152.136, avgs=0 125: dt: 0.9000, rms radial error=151.273, avgs=0 130: dt: 0.9000, rms radial error=150.415, avgs=0 135: dt: 0.9000, rms radial error=149.561, avgs=0 140: dt: 0.9000, rms radial error=148.713, avgs=0 145: dt: 0.9000, rms radial error=147.869, avgs=0 150: dt: 0.9000, rms radial error=147.030, avgs=0 155: dt: 0.9000, rms radial error=146.196, avgs=0 160: dt: 0.9000, rms radial error=145.367, avgs=0 165: dt: 0.9000, rms radial error=144.542, avgs=0 170: dt: 0.9000, rms radial error=143.723, avgs=0 175: dt: 0.9000, rms radial error=142.908, avgs=0 180: dt: 0.9000, rms radial error=142.097, avgs=0 185: dt: 0.9000, rms radial error=141.292, avgs=0 190: dt: 0.9000, rms radial error=140.491, avgs=0 195: dt: 0.9000, rms radial error=139.695, avgs=0 200: dt: 0.9000, rms radial error=138.903, avgs=0 205: dt: 0.9000, rms radial error=138.116, avgs=0 210: dt: 0.9000, rms radial error=137.333, avgs=0 215: dt: 0.9000, rms radial error=136.555, avgs=0 220: dt: 0.9000, rms radial error=135.782, avgs=0 225: dt: 0.9000, rms radial error=135.013, avgs=0 230: dt: 0.9000, rms radial error=134.248, avgs=0 235: dt: 0.9000, rms radial error=133.488, avgs=0 240: dt: 0.9000, rms radial error=132.732, avgs=0 245: dt: 0.9000, rms radial error=131.980, avgs=0 250: dt: 0.9000, rms radial error=131.233, avgs=0 255: dt: 0.9000, rms radial error=130.491, avgs=0 260: dt: 0.9000, rms radial error=129.752, avgs=0 265: dt: 0.9000, rms radial error=129.018, avgs=0 270: dt: 0.9000, rms radial error=128.288, avgs=0 275: dt: 0.9000, rms radial error=127.562, avgs=0 280: dt: 0.9000, rms radial error=126.841, avgs=0 285: dt: 0.9000, rms radial error=126.123, avgs=0 290: dt: 0.9000, rms radial error=125.410, avgs=0 295: dt: 0.9000, rms radial error=124.701, avgs=0 300: dt: 0.9000, rms radial error=123.996, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 98.41 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.26/40 = 0.00647 epoch 2 (K=80.0), pass 1, starting sse = 4.86 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating 365: dt: 3.11, sse: 4.7 (0.123, 10.4, 0.725), neg: 75 (%0.005:%0.02), avgs: 2 366: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 76 (%0.005:%0.02), avgs: 2 367: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 75 (%0.005:%0.02), avgs: 2 368: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 76 (%0.005:%0.02), avgs: 2 369: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 76 (%0.005:%0.02), avgs: 2 370: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 76 (%0.005:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.05-->8.85) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.04-->2.14) 371: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 77 (%0.005:%0.02), avgs: 2 372: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 78 (%0.005:%0.02), avgs: 2 373: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 77 (%0.005:%0.02), avgs: 2 374: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 78 (%0.005:%0.02), avgs: 2 375: dt: 0.09, sse: 4.7 (0.123, 10.4, 0.725), neg: 78 (%0.005:%0.02), avgs: 2 376: dt: 2.26, sse: 4.7 (0.123, 10.4, 0.725), neg: 77 (%0.004:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.05-->8.85) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.04-->2.14) 377: dt: 0.23, sse: 4.7 (0.123, 10.4, 0.725), neg: 75 (%0.004:%0.02), avgs: 0 vertex spacing 2.85 +- 0.99 (0.05-->8.85) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.04-->2.14) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 378: dt: 774.40, sse: 0.7 (0.123, 10.4, 0.725), neg: 72 (%0.004:%0.01), avgs: 32 379: dt: 1030.84, sse: 0.7 (0.123, 10.4, 0.725), neg: 72 (%0.004:%0.02), avgs: 32 380: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 72 (%0.003:%0.01), avgs: 32 vertex spacing 2.85 +- 0.99 (0.02-->8.99) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.03-->2.14) 381: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 71 (%0.003:%0.01), avgs: 32 382: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 72 (%0.003:%0.01), avgs: 32 383: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 72 (%0.003:%0.01), avgs: 32 384: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 72 (%0.003:%0.01), avgs: 32 385: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 73 (%0.003:%0.01), avgs: 32 386: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 73 (%0.003:%0.01), avgs: 32 387: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 73 (%0.003:%0.01), avgs: 32 388: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 73 (%0.003:%0.01), avgs: 32 389: dt: 0.29, sse: 0.7 (0.123, 10.5, 0.725), neg: 72 (%0.003:%0.01), avgs: 32 390: dt: 669.89, sse: 0.7 (0.123, 10.4, 0.725), neg: 71 (%0.003:%0.01), avgs: 32 vertex spacing 2.85 +- 0.99 (0.02-->9.04) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.03-->2.14) vertex spacing 2.85 +- 0.99 (0.02-->9.04) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.03-->2.14) 391: dt: 1.86, sse: 0.7 (0.123, 10.4, 0.725), neg: 73 (%0.003:%0.02), avgs: 8 392: dt: 0.15, sse: 0.7 (0.123, 10.4, 0.725), neg: 73 (%0.003:%0.01), avgs: 8 393: dt: 0.15, sse: 0.7 (0.123, 10.4, 0.725), neg: 73 (%0.003:%0.01), avgs: 8 394: dt: 0.15, sse: 0.7 (0.123, 10.4, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 395: dt: 0.15, sse: 0.7 (0.123, 10.4, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 396: dt: 0.15, sse: 0.7 (0.123, 10.4, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 397: dt: 0.15, sse: 0.7 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 398: dt: 0.15, sse: 0.7 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 399: dt: 0.15, sse: 0.7 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 400: dt: 0.15, sse: 0.7 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 vertex spacing 2.85 +- 0.99 (0.02-->9.04) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.03-->2.14) 401: dt: 0.15, sse: 0.7 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 8 402: dt: 63.44, sse: 0.7 (0.123, 10.4, 0.725), neg: 71 (%0.003:%0.01), avgs: 8 403: dt: 4.21, sse: 0.7 (0.123, 10.4, 0.725), neg: 71 (%0.003:%0.01), avgs: 8 vertex spacing 2.85 +- 0.99 (0.02-->9.05) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.03-->2.14) 404: dt: 0.50, sse: 0.6 (0.123, 10.4, 0.725), neg: 70 (%0.003:%0.01), avgs: 2 405: dt: 4.43, sse: 0.6 (0.123, 10.5, 0.725), neg: 74 (%0.003:%0.02), avgs: 2 406: dt: 0.60, sse: 0.6 (0.123, 10.5, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 407: dt: 0.84, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 408: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 409: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 410: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.02-->9.05) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.02-->2.14) 411: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 412: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 413: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 414: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 415: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 416: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 417: dt: 0.09, sse: 0.6 (0.123, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 418: dt: 1.14, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.02-->9.05) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.02-->2.14) 419: dt: 0.00, sse: 0.6 (0.123, 10.4, 0.725), neg: 73 (%0.002:%0.02), avgs: 0 vertex spacing 2.85 +- 0.99 (0.02-->9.05) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.02-->2.14) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 420: dt: 262.81, sse: 0.2 (0.123, 10.4, 0.725), neg: 70 (%0.002:%0.01), avgs: 32 vertex spacing 2.85 +- 0.99 (0.01-->9.06) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.02-->2.14) 421: dt: 683.20, sse: 0.2 (0.123, 10.5, 0.725), neg: 70 (%0.002:%0.01), avgs: 32 422: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 423: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 424: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 425: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 426: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 427: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 428: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 429: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 430: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 vertex spacing 2.85 +- 0.99 (0.01-->9.09) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.02-->2.14) 431: dt: 0.29, sse: 0.2 (0.123, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 32 432: dt: 217.18, sse: 0.2 (0.124, 10.4, 0.725), neg: 67 (%0.002:%0.01), avgs: 32 433: dt: 1303.07, sse: 0.2 (0.124, 10.4, 0.725), neg: 68 (%0.002:%0.01), avgs: 32 vertex spacing 2.85 +- 0.99 (0.01-->9.15) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.02-->2.14) 434: dt: 11.52, sse: 0.2 (0.124, 10.5, 0.725), neg: 68 (%0.002:%0.01), avgs: 8 435: dt: 2.52, sse: 0.2 (0.124, 10.4, 0.725), neg: 67 (%0.002:%0.01), avgs: 8 436: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 68 (%0.002:%0.01), avgs: 8 437: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 8 438: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 8 439: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 8 440: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 70 (%0.002:%0.01), avgs: 8 vertex spacing 2.85 +- 0.99 (0.01-->9.15) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.01-->2.14) 441: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 70 (%0.002:%0.01), avgs: 8 442: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 68 (%0.002:%0.01), avgs: 8 443: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 68 (%0.002:%0.01), avgs: 8 444: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 8 445: dt: 0.15, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 8 446: dt: 11.39, sse: 0.2 (0.124, 10.5, 0.725), neg: 71 (%0.002:%0.01), avgs: 8 vertex spacing 2.85 +- 0.99 (0.01-->9.16) (max @ vno 9866 --> 9508) face area 0.30 +- 0.20 (-0.01-->2.14) 447: dt: 0.00, sse: 0.2 (0.124, 10.5, 0.725), neg: 71 (%0.002:%0.01), avgs: 2 448: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 69 (%0.002:%0.01), avgs: 2 449: dt: 0.09, sse: 0.2 (0.124, 10.5, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 450: dt: 0.09, sse: 0.2 (0.124, 10.5, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 vertex spacing 2.85 +- 0.99 (0.01-->9.16) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.01-->2.14) 451: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 452: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 71 (%0.002:%0.01), avgs: 2 453: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 72 (%0.002:%0.01), avgs: 2 454: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 72 (%0.001:%0.01), avgs: 2 455: dt: 0.09, sse: 0.2 (0.124, 10.4, 0.725), neg: 72 (%0.001:%0.01), avgs: 2 456: dt: 0.09, sse: 0.2 (0.124, 10.5, 0.725), neg: 73 (%0.001:%0.01), avgs: 2 457: dt: 0.09, sse: 0.2 (0.124, 10.5, 0.725), neg: 74 (%0.001:%0.02), avgs: 2 458: dt: 0.00, sse: 0.2 (0.124, 10.5, 0.725), neg: 74 (%0.001:%0.02), avgs: 2 vertex spacing 2.85 +- 0.99 (0.00-->9.16) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.01-->2.14) 459: dt: 0.00, sse: 0.2 (0.124, 10.5, 0.725), neg: 74 (%0.001:%0.02), avgs: 0 vertex spacing 2.85 +- 0.99 (0.00-->9.16) (max @ vno 9508 --> 9866) face area 0.30 +- 0.20 (-0.01-->2.14) 459: dt: 0.00, sse: 73.2 (0.124, 10.5, 0.725), neg: 74 (%0.001:%0.02), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.03 hours with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.04/37 = 0.00116 epoch 3 (K=320.0), pass 1, starting sse = 0.76 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.21/42 = 0.00505 epoch 4 (K=1280.0), pass 1, starting sse = 0.23 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.27/40 = 0.00663 final distance error %100000.00 optimization complete. unfolding took 0.02 hours #-------------------------------------------- #@# Fix Topology lh Wed Oct 17 01:04:30 CDT 2007 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga 990903_61167 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* 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 1.41.2.1 2007/01/05 16:58:33 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ before topology correction, eno=4 (nv=14999, nf=30036, ne=45031, g=-1) 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... 286 ambiguous faces found in tessellation segmenting defects... 15 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 1 into 2 14 defects to be corrected 0 vertices coincident vertex 2830: degenerate normal vertex 7693: degenerate normal vertex 2830: degenerate normal vertex 7693: degenerate normal vertex 2830: degenerate normal vertex 7693: degenerate normal Computing Initial Surface Statistics -face loglikelihood: -9.7950 (-4.8975) -vertex loglikelihood: -8.6685 (-4.3343) -normal dot loglikelihood: -3.6067 (-3.6067) -quad curv loglikelihood: -6.2198 (-3.1099) Total Loglikelihood : -28.2900 CORRECTING DEFECT 0 (vertices=10, convex hull=34) l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 After retessellation of defect 0, euler #=-12 (14783,44133,29338) : difference with theory (-11) = 1 CORRECTING DEFECT 1 (vertices=24, convex hull=69) After retessellation of defect 1, euler #=-10 (14792,44191,29389) : difference with theory (-10) = 0 CORRECTING DEFECT 2 (vertices=11, convex hull=37) After retessellation of defect 2, euler #=-9 (14800,44224,29415) : difference with theory (-9) = 0 CORRECTING DEFECT 3 (vertices=22, convex hull=63) After retessellation of defect 3, euler #=-8 (14808,44272,29456) : difference with theory (-8) = 0 CORRECTING DEFECT 4 (vertices=14, convex hull=20) After retessellation of defect 4, euler #=-7 (14809,44279,29463) : difference with theory (-7) = 0 CORRECTING DEFECT 5 (vertices=17, convex hull=47) After retessellation of defect 5, euler #=-6 (14818,44325,29501) : difference with theory (-6) = 0 CORRECTING DEFECT 6 (vertices=11, convex hull=33) After retessellation of defect 6, euler #=-5 (14825,44359,29529) : difference with theory (-5) = 0 CORRECTING DEFECT 7 (vertices=17, convex hull=46) After retessellation of defect 7, euler #=-4 (14836,44406,29566) : difference with theory (-4) = 0 CORRECTING DEFECT 8 (vertices=19, convex hull=42) After retessellation of defect 8, euler #=-3 (14847,44453,29603) : difference with theory (-3) = 0 CORRECTING DEFECT 9 (vertices=13, convex hull=50) After retessellation of defect 9, euler #=-2 (14853,44488,29633) : difference with theory (-2) = 0 CORRECTING DEFECT 10 (vertices=29, convex hull=66) After retessellation of defect 10, euler #=-1 (14867,44557,29689) : difference with theory (-1) = 0 CORRECTING DEFECT 11 (vertices=11, convex hull=43) After retessellation of defect 11, euler #=0 (14874,44590,29716) : difference with theory (0) = 0 CORRECTING DEFECT 12 (vertices=8, convex hull=26) After retessellation of defect 12, euler #=1 (14876,44602,29727) : difference with theory (1) = 0 CORRECTING DEFECT 13 (vertices=16, convex hull=46) After retessellation of defect 13, euler #=2 (14885,44649,29766) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.22 (0.03-->2.52) (max @ vno 8640 --> 8969) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.22 (0.03-->2.52) (max @ vno 8640 --> 8969) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 55 mutations (37.4%), 92 crossovers (62.6%), 8 vertices were eliminated building final representation... 114 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=14885, nf=29766, ne=44649, g=0) writing corrected surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 5.9 minutes reading input surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... 0 defective edges removing intersecting faces 000: 10 intersecting 001: 2 intersecting /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 10 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make Final Surf lh Wed Oct 17 01:10:30 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_make_surfaces -mgz -T1 brain.finalsurfs 990903_61167 lh INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/filled.mgz... reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/brain.finalsurfs.mgz... reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/wm.mgz... 10150 bright wm thresholded. 320 bright non-wm voxels segmented. reading original surface position from /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.orig... computing class statistics... border white: 20018 voxels (0.12%) border gray 17816 voxels (0.11%) WM: 100.7 +- 8.2 [70.0 --> 110.0] GM: 86.5 +- 18.1 [40.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to -17.1 (was 70) setting MAX_BORDER_WHITE to 110.2 (was 105) setting MIN_BORDER_WHITE to 1.0 (was 85) setting MAX_CSF to -35.1 (was 40) setting MAX_GRAY to 93.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to -8.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to -53.2 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.85 +- 0.22 (0.05-->2.08) (max @ vno 8969 --> 8640) face area 0.30 +- 0.13 (0.00-->1.12) mean absolute distance = 1.21 +- 1.82 681 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=102, GM=1 using class modes intead of means.... mean inside = 96.9, mean outside = 59.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=64.7, 136 (136) missing vertices, mean dist 0.8 [0.6 (%35.4)->1.5 (%64.6))] %78 local maxima, % 1 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=4, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.96 +- 0.27 (0.09-->2.72) (max @ vno 3959 --> 4253) face area 0.30 +- 0.14 (0.00-->1.52) vertex spacing 0.98 +- 0.30 (0.09-->3.60) (max @ vno 3959 --> 4253) face area 0.30 +- 0.16 (0.00-->2.64) vertex spacing 0.97 +- 0.32 (0.12-->4.36) (max @ vno 3959 --> 4253) face area 0.30 +- 0.17 (0.00-->3.03) vertex spacing 0.96 +- 0.32 (0.12-->4.56) (max @ vno 3959 --> 4253) face area 0.30 +- 0.17 (0.00-->3.09) smoothing T1 volume with sigma = 1.000 vertex spacing 0.96 +- 0.32 (0.17-->4.64) (max @ vno 3959 --> 4253) face area 0.30 +- 0.17 (0.00-->3.16) mean absolute distance = 0.41 +- 0.96 395 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=556968.5, rms=30.31 001: dt: 0.5000, sse=938040.9, rms=23.85 002: dt: 0.5000, sse=1161017.1, rms=20.92 003: dt: 0.5000, sse=1243549.1, rms=19.48 004: dt: 0.5000, sse=1295267.0, rms=18.89 005: dt: 0.5000, sse=1309482.6, rms=18.25 006: dt: 0.5000, sse=1318864.0, rms=18.00 007: dt: 0.5000, sse=1342170.8, rms=17.41 008: dt: 0.5000, sse=1325973.2, rms=17.24 009: dt: 0.5000, sse=1330782.4, rms=16.60 010: dt: 0.5000, sse=1321693.0, rms=16.43 011: dt: 0.5000, sse=1326841.4, rms=15.91 012: dt: 0.5000, sse=1310906.2, rms=15.86 013: dt: 0.5000, sse=1318990.1, rms=15.57 rms = 15.59, time step reduction 1 of 3 to 0.250... 014: dt: 0.2500, sse=1042701.7, rms=12.20 rms = 13.85, time step reduction 2 of 3 to 0.125... 015: dt: 0.1250, sse=963779.6, rms=11.24 016: dt: 0.1250, sse=847185.3, rms=10.14 017: dt: 0.1250, sse=838650.6, rms=9.89 018: dt: 0.1250, sse=841265.8, rms=9.72 019: dt: 0.1250, sse=833296.6, rms=9.65 020: dt: 0.1250, sse=830798.9, rms=9.57 021: dt: 0.1250, sse=833688.0, rms=9.47 rms = 9.46, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=827982.9, rms=9.46 positioning took 3.0 minutes inhibiting deformation at non-cortical midline structures... mean border=60.8, 214 (25) missing vertices, mean dist 0.2 [0.3 (%38.7)->0.5 (%61.3))] %77 local maxima, % 0 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=2, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.96 +- 0.32 (0.17-->4.72) (max @ vno 3959 --> 4253) face area 0.37 +- 0.21 (0.00-->3.89) smoothing T1 volume with sigma = 0.500 vertex spacing 0.96 +- 0.32 (0.18-->4.78) (max @ vno 3959 --> 4253) face area 0.37 +- 0.22 (0.00-->3.88) mean absolute distance = 0.28 +- 0.74 263 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=880444.6, rms=13.67 rms = 17.32, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=860003.8, rms=11.51 rms = 13.21, time step reduction 2 of 3 to 0.125... 024: dt: 0.1250, sse=834499.1, rms=10.94 025: dt: 0.1250, sse=811251.8, rms=10.14 026: dt: 0.1250, sse=824126.7, rms=9.91 rms = 9.88, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=829081.1, rms=9.88 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... mean border=60.8, 293 (16) missing vertices, mean dist 0.1 [0.2 (%48.3)->0.4 (%51.7))] %77 local maxima, % 0 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=1, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.96 +- 0.32 (0.13-->4.83) (max @ vno 3959 --> 4253) face area 0.37 +- 0.22 (0.00-->3.88) smoothing T1 volume with sigma = 0.250 vertex spacing 0.96 +- 0.32 (0.13-->4.83) (max @ vno 3959 --> 4253) face area 0.37 +- 0.22 (0.00-->3.88) mean absolute distance = 0.21 +- 0.50 286 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=830132.8, rms=10.03 rms = 18.57, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=837464.8, rms=9.36 rms = 12.29, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=828127.6, rms=9.08 rms = 9.03, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=852993.2, rms=9.03 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... mean border=60.6, 430 (16) missing vertices, mean dist 0.0 [0.2 (%48.1)->0.3 (%51.9))] %76 local maxima, % 0 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=0, nbrs=2, l_repulse=1.000, 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 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.white... writing smoothed curvature to lh.curv writing smoothed area to lh.area vertex spacing 0.97 +- 0.32 (0.14-->4.85) (max @ vno 3959 --> 4253) face area 0.37 +- 0.22 (0.00-->3.86) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=852326.2, rms=8.96 rms = 17.07, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=889436.2, rms=8.49 rms = 12.39, time step reduction 2 of 3 to 0.125... 032: dt: 0.1250, sse=882086.0, rms=8.10 033: dt: 0.1250, sse=917776.9, rms=7.81 rms = 7.88, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=917776.9, rms=7.81 positioning took 0.5 minutes generating cortex label... writing cortex label to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/label/lh.cortex.label... LabelWrite: saving to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/label/lh.cortex.label writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.curv writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.area smoothing surface for 5 iterations... mean border=13.8, 1088 (1088) missing vertices, mean dist 0.0 [0.0 (%nan)->0.0 (%nan))] % 0 local maxima, % 0 large gradients and %72 min vals, 0 gradients ignored tol=1.0e-04, host=vader, 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 vertex spacing 0.97 +- 0.38 (0.05-->6.27) (max @ vno 3959 --> 4253) face area 0.32 +- 0.22 (0.00-->3.90) vertex spacing 1.00 +- 0.44 (0.04-->6.34) (max @ vno 3959 --> 4253) face area 0.32 +- 0.25 (0.00-->4.23) vertex spacing 1.01 +- 0.49 (0.04-->6.80) (max @ vno 3959 --> 4253) face area 0.32 +- 0.27 (0.00-->4.74) vertex spacing 1.02 +- 0.52 (0.05-->6.98) (max @ vno 3138 --> 3137) face area 0.32 +- 0.29 (0.00-->5.68) vertex spacing 1.03 +- 0.56 (0.05-->7.73) (max @ vno 3138 --> 3137) face area 0.32 +- 0.31 (0.00-->5.28) vertex spacing 1.03 +- 0.58 (0.05-->8.93) (max @ vno 14855 --> 14859) face area 0.32 +- 0.32 (0.00-->5.73) smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=1636650.6, rms=58.63 001: dt: 0.5000, sse=1013620.6, rms=43.33 002: dt: 0.5000, sse=683617.4, rms=31.37 003: dt: 0.5000, sse=597356.9, rms=24.63 004: dt: 0.5000, sse=639819.4, rms=21.71 005: dt: 0.5000, sse=677885.0, rms=20.39 006: dt: 0.5000, sse=682027.6, rms=19.62 007: dt: 0.5000, sse=677096.1, rms=18.89 008: dt: 0.5000, sse=683559.8, rms=18.33 009: dt: 0.5000, sse=705112.8, rms=17.90 010: dt: 0.5000, sse=696687.4, rms=17.74 011: dt: 0.5000, sse=713454.1, rms=17.34 012: dt: 0.5000, sse=690673.8, rms=17.11 013: dt: 0.5000, sse=673650.8, rms=16.77 014: dt: 0.5000, sse=672526.9, rms=16.59 015: dt: 0.5000, sse=660376.5, rms=16.34 016: dt: 0.5000, sse=649383.6, rms=16.27 017: dt: 0.5000, sse=670806.3, rms=16.09 018: dt: 0.5000, sse=645912.7, rms=15.97 019: dt: 0.5000, sse=654089.6, rms=15.77 020: dt: 0.5000, sse=648822.0, rms=15.58 021: dt: 0.5000, sse=651511.5, rms=15.37 022: dt: 0.5000, sse=659019.6, rms=15.27 023: dt: 0.5000, sse=652866.9, rms=15.18 024: dt: 0.5000, sse=655090.2, rms=15.08 025: dt: 0.5000, sse=658881.8, rms=14.88 rms = 14.86, time step reduction 1 of 3 to 0.250... 026: dt: 0.5000, sse=656174.4, rms=14.86 027: dt: 0.2500, sse=602901.3, rms=14.68 028: dt: 0.2500, sse=584109.6, rms=14.61 rms = 14.60, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=594833.8, rms=14.60 rms = 14.57, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=566477.8, rms=14.57 positioning took 3.8 minutes mean border=12.5, 1641 (672) missing vertices, mean dist 0.0 [0.0 (%nan)->0.0 (%nan))] % 0 local maxima, % 0 large gradients and %68 min vals, 0 gradients ignored tol=1.0e-04, host=vader, 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=630343.1, rms=17.30 rms = 17.63, time step reduction 1 of 3 to 0.250... rms = 17.25, time step reduction 2 of 3 to 0.125... 031: dt: 0.2500, sse=610829.6, rms=17.25 rms = 17.26, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=610829.6, rms=17.25 positioning took 0.3 minutes mean border=12.2, 1926 (655) missing vertices, mean dist 0.0 [0.0 (%nan)->0.0 (%nan))] % 0 local maxima, % 0 large gradients and %66 min vals, 0 gradients ignored tol=1.0e-04, host=vader, 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=610924.6, rms=17.25 rms = 17.50, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=607303.9, rms=17.17 rms = 17.19, time step reduction 2 of 3 to 0.125... rms = 17.15, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=602180.1, rms=17.15 positioning took 0.4 minutes mean border=10.9, 2346 (641) missing vertices, mean dist 0.0 [0.0 (%nan)->0.0 (%nan))] % 0 local maxima, % 0 large gradients and %63 min vals, 0 gradients ignored tol=1.0e-04, host=vader, 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 vertex spacing 1.03 +- 0.58 (0.05-->9.18) (max @ vno 14859 --> 14855) face area 0.42 +- 0.41 (0.00-->7.54) vertex spacing 1.04 +- 0.58 (0.05-->10.41) (max @ vno 9595 --> 9252) face area 0.42 +- 0.41 (0.00-->7.23) vertex spacing 1.05 +- 0.59 (0.05-->11.21) (max @ vno 9595 --> 9252) face area 0.42 +- 0.42 (0.00-->7.30) writing pial surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.pial... writing smoothed curvature to lh.curv.pial writing smoothed area to lh.area.pial vertex spacing 1.04 +- 0.59 (0.05-->10.83) (max @ vno 9252 --> 9595) face area 0.42 +- 0.42 (0.00-->7.35) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. positioning took 16.5 minutes 000: dt: 0.0000, sse=598699.8, rms=16.91 rms = 17.16, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=611604.9, rms=16.79 036: dt: 0.2500, sse=714832.4, rms=16.63 037: dt: 0.2500, sse=743225.4, rms=16.26 038: dt: 0.2500, sse=778444.4, rms=15.99 039: dt: 0.2500, sse=790221.7, rms=15.83 040: dt: 0.2500, sse=827716.0, rms=15.73 041: dt: 0.2500, sse=831538.2, rms=15.64 042: dt: 0.2500, sse=842668.0, rms=15.58 043: dt: 0.2500, sse=838170.6, rms=15.50 044: dt: 0.2500, sse=853006.9, rms=15.42 rms = 15.42, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=840994.2, rms=15.42 046: dt: 0.1250, sse=809377.4, rms=15.32 047: dt: 0.1250, sse=796825.4, rms=15.26 rms = 15.22, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=808885.5, rms=15.22 positioning took 1.6 minutes writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.curv.pial writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.area.pial 0 of 14885 vertices processed 0 of 14885 vertices processed thickness calculation complete, 481:743 truncations. 7877 vertices at 0 distance 8033 vertices at 1 distance 4544 vertices at 2 distance 1956 vertices at 3 distance 689 vertices at 4 distance 228 vertices at 5 distance 93 vertices at 6 distance 37 vertices at 7 distance 33 vertices at 8 distance 14 vertices at 9 distance 13 vertices at 10 distance 6 vertices at 11 distance 4 vertices at 12 distance 10 vertices at 13 distance 14 vertices at 14 distance 7 vertices at 15 distance 4 vertices at 16 distance 0 vertices at 17 distance 0 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.thickness #-------------------------------------------- #@# Smooth2 lh Wed Oct 17 01:26:58 CDT 2007 mris_smooth -n 3 -nw ../surf/lh.white ../surf/lh.smoothwm /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts smoothing for 3 iterations smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Wed Oct 17 01:26:59 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 24.8 mm, total surface area = 9854 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation took 0.1 minutes step 000: RMS=0.151 (target=0.015) step 005: RMS=0.097 (target=0.015) step 010: RMS=0.083 (target=0.015) step 015: RMS=0.075 (target=0.015) step 020: RMS=0.071 (target=0.015) step 025: RMS=0.061 (target=0.015) step 030: RMS=0.054 (target=0.015) step 035: RMS=0.050 (target=0.015) step 040: RMS=0.045 (target=0.015) step 045: RMS=0.045 (target=0.015) step 050: RMS=0.046 (target=0.015) step 055: RMS=0.045 (target=0.015) step 060: RMS=0.043 (target=0.015) inflation complete. #-------------------------------------------- #@# Cortical ribbon mask lh Wed Oct 17 01:27:08 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_surf2vol --mkmask --hemi lh --fillribbon --template orig.mgz --volregidentity 990903_61167 --outvol lh.ribbon.mgz gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: ------------------------------ -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; -------------------------------------------------- subjects dir /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE hemi lh mksurfmask 1 projfrac 0 volreg file (null) outvol path lh.ribbon.mgz template path orig.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = 0.000000 0.000000 0.000000 Gdiag_no -1 Reading surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.white Done reading source surface Reading thickness /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/lh.thickness Done surf nframes = 1 INFO: mapping vertices to closest voxel INFO: resampling surface to volume at projfrac=0.00, 9945 hits INFO: resampling surface to volume at projfrac=0.05, 9923 hits INFO: resampling surface to volume at projfrac=0.10, 9954 hits INFO: resampling surface to volume at projfrac=0.15, 9906 hits INFO: resampling surface to volume at projfrac=0.20, 9870 hits INFO: resampling surface to volume at projfrac=0.25, 9912 hits INFO: resampling surface to volume at projfrac=0.30, 9969 hits INFO: resampling surface to volume at projfrac=0.35, 9980 hits INFO: resampling surface to volume at projfrac=0.40, 9947 hits INFO: resampling surface to volume at projfrac=0.45, 9934 hits INFO: resampling surface to volume at projfrac=0.50, 9903 hits INFO: resampling surface to volume at projfrac=0.55, 9888 hits INFO: resampling surface to volume at projfrac=0.60, 9852 hits INFO: resampling surface to volume at projfrac=0.65, 9808 hits INFO: resampling surface to volume at projfrac=0.70, 9752 hits INFO: resampling surface to volume at projfrac=0.75, 9748 hits INFO: resampling surface to volume at projfrac=0.80, 9704 hits INFO: resampling surface to volume at projfrac=0.85, 9641 hits INFO: resampling surface to volume at projfrac=0.90, 9629 hits INFO: resampling surface to volume at projfrac=0.95, 9635 hits INFO: writing output volume to lh.ribbon.mgz done #-------------------------------------------- #@# Tessellate rh Wed Oct 17 01:28:01 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mri_tessellate ../mri/filled.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ slice 210: 59 vertices, 73 faces slice 220: 1245 vertices, 1334 faces slice 230: 3666 vertices, 3801 faces slice 240: 8162 vertices, 8256 faces slice 250: 8284 vertices, 8320 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using ras2vox 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; #-------------------------------------------- #@# Smooth1 rh Wed Oct 17 01:31:46 CDT 2007 mris_smooth -nw ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Wed Oct 17 01:31:46 CDT 2007 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts avg radius = 22.1 mm, total surface area = 5250 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.1 minutes Not saving sulc step 000: RMS=0.155 (target=0.015) step 005: RMS=0.125 (target=0.015) step 010: RMS=0.105 (target=0.015) step 015: RMS=0.095 (target=0.015) step 020: RMS=0.090 (target=0.015) step 025: RMS=0.087 (target=0.015) step 030: RMS=0.086 (target=0.015) step 035: RMS=0.084 (target=0.015) step 040: RMS=0.083 (target=0.015) step 045: RMS=0.081 (target=0.015) step 050: RMS=0.082 (target=0.015) step 055: RMS=0.084 (target=0.015) step 060: RMS=0.083 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed Oct 17 01:31:51 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_sphere -q ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, host=vader, nav=0, nbrs=1, l_spring_norm=1.000, l_sphere=0.025, l_convex=1.000 mom=0.90, dt=0.90 surface projected - minimizing metric distortion... vertex spacing 3.55 +- 1.88 (0.07-->10.61) (max @ vno 2338 --> 2339) face area 0.32 +- 0.30 (-0.41-->2.11) tol=1.0e-01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 301: dt: 563.69, sse: 100.3 (0.209, 16.4, 0.744), neg: 136 (%0.065:%0.27), avgs: 32 302: dt: 156.37, sse: 95.6 (0.207, 15.1, 0.744), neg: 111 (%0.068:%0.14), avgs: 32 303: dt: 602.02, sse: 86.6 (0.212, 16.7, 0.751), neg: 130 (%0.064:%0.18), avgs: 32 304: dt: 254.62, sse: 83.7 (0.213, 16.6, 0.753), neg: 121 (%0.069:%0.15), avgs: 32 305: dt: 636.83, sse: 79.3 (0.221, 17.8, 0.762), neg: 112 (%0.065:%0.18), avgs: 32 306: dt: 327.89, sse: 76.5 (0.221, 18.3, 0.765), neg: 115 (%0.069:%0.15), avgs: 32 307: dt: 673.97, sse: 73.4 (0.227, 19.4, 0.773), neg: 118 (%0.067:%0.15), avgs: 32 308: dt: 400.39, sse: 71.4 (0.227, 19.9, 0.777), neg: 124 (%0.070:%0.16), avgs: 32 309: dt: 0.29, sse: 71.4 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 310: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 vertex spacing 3.82 +- 1.84 (0.03-->19.21) (max @ vno 1983 --> 1981) face area 0.32 +- 0.30 (-0.22-->3.18) 311: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 312: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 313: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 314: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 315: dt: 0.29, sse: 71.5 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 316: dt: 0.29, sse: 71.6 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 317: dt: 0.29, sse: 71.6 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 318: dt: 0.29, sse: 71.6 (0.227, 19.9, 0.776), neg: 124 (%0.070:%0.16), avgs: 32 319: dt: 529.75, sse: 70.6 (0.229, 20.5, 0.783), neg: 123 (%0.070:%0.21), avgs: 32 vertex spacing 3.85 +- 1.86 (0.03-->19.88) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.17-->3.24) 320: dt: 6.89, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.062:%0.15), avgs: 8 vertex spacing 3.85 +- 1.86 (0.03-->19.92) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.16-->3.24) 321: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.062:%0.15), avgs: 8 322: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.062:%0.15), avgs: 8 323: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.062:%0.15), avgs: 8 324: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.061:%0.15), avgs: 8 325: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.061:%0.15), avgs: 8 326: dt: 0.15, sse: 69.9 (0.229, 20.5, 0.783), neg: 121 (%0.061:%0.15), avgs: 8 327: dt: 0.15, sse: 69.8 (0.229, 20.5, 0.783), neg: 121 (%0.061:%0.15), avgs: 8 328: dt: 0.15, sse: 69.8 (0.229, 20.5, 0.783), neg: 121 (%0.061:%0.15), avgs: 8 329: dt: 0.15, sse: 69.8 (0.229, 20.5, 0.783), neg: 121 (%0.060:%0.15), avgs: 8 330: dt: 0.15, sse: 69.7 (0.229, 20.5, 0.783), neg: 121 (%0.060:%0.15), avgs: 8 vertex spacing 3.85 +- 1.86 (0.03-->19.94) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.15-->3.24) 331: dt: 79.01, sse: 68.6 (0.229, 20.8, 0.784), neg: 123 (%0.049:%0.16), avgs: 8 vertex spacing 3.86 +- 1.86 (0.03-->20.33) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.08-->3.24) 332: dt: 8.04, sse: 67.8 (0.229, 20.7, 0.784), neg: 116 (%0.035:%0.15), avgs: 2 333: dt: 4.24, sse: 67.4 (0.229, 20.6, 0.784), neg: 120 (%0.035:%0.15), avgs: 2 334: dt: 0.09, sse: 67.4 (0.229, 20.7, 0.784), neg: 121 (%0.035:%0.15), avgs: 2 335: dt: 0.09, sse: 67.4 (0.229, 20.7, 0.784), neg: 121 (%0.035:%0.15), avgs: 2 336: dt: 0.09, sse: 67.4 (0.229, 20.7, 0.784), neg: 122 (%0.035:%0.15), avgs: 2 337: dt: 0.09, sse: 67.3 (0.229, 20.7, 0.784), neg: 122 (%0.034:%0.15), avgs: 2 338: dt: 0.09, sse: 67.3 (0.229, 20.7, 0.784), neg: 123 (%0.034:%0.16), avgs: 2 339: dt: 0.09, sse: 67.3 (0.229, 20.7, 0.784), neg: 124 (%0.033:%0.16), avgs: 2 340: dt: 0.09, sse: 67.2 (0.229, 20.7, 0.784), neg: 124 (%0.033:%0.16), avgs: 2 vertex spacing 3.86 +- 1.86 (0.03-->20.35) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.06-->3.24) 341: dt: 0.09, sse: 67.2 (0.229, 20.7, 0.784), neg: 123 (%0.032:%0.15), avgs: 2 342: dt: 0.09, sse: 67.1 (0.229, 20.7, 0.784), neg: 123 (%0.032:%0.15), avgs: 2 343: dt: 0.09, sse: 67.1 (0.229, 20.7, 0.784), neg: 123 (%0.032:%0.15), avgs: 2 344: dt: 21.66, sse: 66.2 (0.230, 20.8, 0.784), neg: 128 (%0.032:%0.18), avgs: 2 345: dt: 1.22, sse: 65.9 (0.230, 20.7, 0.784), neg: 128 (%0.028:%0.14), avgs: 2 vertex spacing 3.86 +- 1.86 (0.03-->20.35) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.06-->3.24) 346: dt: 1.24, sse: 65.7 (0.230, 20.7, 0.784), neg: 126 (%0.026:%0.13), avgs: 0 vertex spacing 3.86 +- 1.86 (0.03-->20.35) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.10-->3.24) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 347: dt: 534.83, sse: 5.3 (0.231, 20.8, 0.785), neg: 125 (%0.024:%0.13), avgs: 32 348: dt: 0.29, sse: 5.3 (0.231, 20.8, 0.785), neg: 122 (%0.024:%0.13), avgs: 32 349: dt: 0.29, sse: 5.3 (0.231, 20.8, 0.785), neg: 122 (%0.024:%0.13), avgs: 32 350: dt: 0.29, sse: 5.3 (0.231, 20.8, 0.785), neg: 121 (%0.023:%0.13), avgs: 32 vertex spacing 3.87 +- 1.86 (0.01-->20.46) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.11-->3.25) 351: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.785), neg: 126 (%0.024:%0.13), avgs: 32 352: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.785), neg: 127 (%0.023:%0.13), avgs: 32 353: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.785), neg: 127 (%0.023:%0.13), avgs: 32 354: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.786), neg: 127 (%0.023:%0.13), avgs: 32 355: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.786), neg: 127 (%0.023:%0.13), avgs: 32 356: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.786), neg: 126 (%0.023:%0.13), avgs: 32 357: dt: 0.29, sse: 5.3 (0.231, 20.9, 0.786), neg: 125 (%0.023:%0.13), avgs: 32 358: dt: 347.23, sse: 5.3 (0.232, 21.0, 0.787), neg: 124 (%0.023:%0.13), avgs: 32 vertex spacing 3.87 +- 1.87 (0.03-->20.52) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.14-->3.26) 359: dt: 60.50, sse: 5.2 (0.232, 21.1, 0.787), neg: 125 (%0.019:%0.12), avgs: 8 360: dt: 43.37, sse: 5.1 (0.232, 21.2, 0.787), neg: 123 (%0.017:%0.12), avgs: 8 vertex spacing 3.87 +- 1.87 (0.02-->20.55) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.04-->3.27) 361: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 123 (%0.017:%0.11), avgs: 8 362: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 124 (%0.017:%0.11), avgs: 8 363: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 122 (%0.017:%0.11), avgs: 8 364: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 122 (%0.017:%0.11), avgs: 8 365: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 122 (%0.017:%0.11), avgs: 8 366: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 121 (%0.017:%0.11), avgs: 8 367: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 123 (%0.017:%0.12), avgs: 8 368: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 122 (%0.017:%0.12), avgs: 8 369: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 124 (%0.017:%0.12), avgs: 8 370: dt: 0.15, sse: 5.1 (0.232, 21.2, 0.787), neg: 124 (%0.017:%0.12), avgs: 8 vertex spacing 3.87 +- 1.87 (0.02-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.04-->3.27) 371: dt: 31.58, sse: 5.0 (0.232, 21.2, 0.787), neg: 122 (%0.016:%0.11), avgs: 8 vertex spacing 3.87 +- 1.87 (0.02-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.04-->3.27) inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.428, avgs=0 005: dt: 0.9000, rms radial error=177.176, avgs=0 010: dt: 0.9000, rms radial error=176.634, avgs=0 015: dt: 0.9000, rms radial error=175.923, avgs=0 020: dt: 0.9000, rms radial error=175.111, avgs=0 025: dt: 0.9000, rms radial error=174.240, avgs=0 030: dt: 0.9000, rms radial error=173.336, avgs=0 035: dt: 0.9000, rms radial error=172.413, avgs=0 040: dt: 0.9000, rms radial error=171.479, avgs=0 045: dt: 0.9000, rms radial error=170.539, avgs=0 050: dt: 0.9000, rms radial error=169.599, avgs=0 055: dt: 0.9000, rms radial error=168.658, avgs=0 060: dt: 0.9000, rms radial error=167.719, avgs=0 065: dt: 0.9000, rms radial error=166.783, avgs=0 070: dt: 0.9000, rms radial error=165.850, avgs=0 075: dt: 0.9000, rms radial error=164.920, avgs=0 080: dt: 0.9000, rms radial error=163.993, avgs=0 085: dt: 0.9000, rms radial error=163.072, avgs=0 090: dt: 0.9000, rms radial error=162.154, avgs=0 095: dt: 0.9000, rms radial error=161.241, avgs=0 100: dt: 0.9000, rms radial error=160.332, avgs=0 105: dt: 0.9000, rms radial error=159.427, avgs=0 110: dt: 0.9000, rms radial error=158.527, avgs=0 115: dt: 0.9000, rms radial error=157.632, avgs=0 120: dt: 0.9000, rms radial error=156.742, avgs=0 125: dt: 0.9000, rms radial error=155.856, avgs=0 130: dt: 0.9000, rms radial error=154.975, avgs=0 135: dt: 0.9000, rms radial error=154.099, avgs=0 140: dt: 0.9000, rms radial error=153.228, avgs=0 145: dt: 0.9000, rms radial error=152.362, avgs=0 150: dt: 0.9000, rms radial error=151.501, avgs=0 155: dt: 0.9000, rms radial error=150.644, avgs=0 160: dt: 0.9000, rms radial error=149.793, avgs=0 165: dt: 0.9000, rms radial error=148.946, avgs=0 170: dt: 0.9000, rms radial error=148.105, avgs=0 175: dt: 0.9000, rms radial error=147.268, avgs=0 180: dt: 0.9000, rms radial error=146.436, avgs=0 185: dt: 0.9000, rms radial error=145.608, avgs=0 190: dt: 0.9000, rms radial error=144.786, avgs=0 195: dt: 0.9000, rms radial error=143.968, avgs=0 200: dt: 0.9000, rms radial error=143.155, avgs=0 205: dt: 0.9000, rms radial error=142.347, avgs=0 210: dt: 0.9000, rms radial error=141.543, avgs=0 215: dt: 0.9000, rms radial error=140.744, avgs=0 220: dt: 0.9000, rms radial error=139.950, avgs=0 225: dt: 0.9000, rms radial error=139.160, avgs=0 230: dt: 0.9000, rms radial error=138.375, avgs=0 235: dt: 0.9000, rms radial error=137.595, avgs=0 240: dt: 0.9000, rms radial error=136.819, avgs=0 245: dt: 0.9000, rms radial error=136.048, avgs=0 250: dt: 0.9000, rms radial error=135.282, avgs=0 255: dt: 0.9000, rms radial error=134.520, avgs=0 260: dt: 0.9000, rms radial error=133.762, avgs=0 265: dt: 0.9000, rms radial error=133.009, avgs=0 270: dt: 0.9000, rms radial error=132.260, avgs=0 275: dt: 0.9000, rms radial error=131.516, avgs=0 280: dt: 0.9000, rms radial error=130.777, avgs=0 285: dt: 0.9000, rms radial error=130.041, avgs=0 290: dt: 0.9000, rms radial error=129.310, avgs=0 295: dt: 0.9000, rms radial error=128.584, avgs=0 300: dt: 0.9000, rms radial error=127.861, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 113.02 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.42/46 = 0.00911 epoch 2 (K=80.0), pass 1, starting sse = 5.40 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating372: dt: 3.92, sse: 5.0 (0.232, 21.2, 0.787), neg: 124 (%0.015:%0.12), avgs: 2 373: dt: 2.42, sse: 4.9 (0.232, 21.2, 0.787), neg: 118 (%0.014:%0.11), avgs: 2 374: dt: 1.83, sse: 4.9 (0.232, 21.2, 0.787), neg: 116 (%0.013:%0.11), avgs: 2 375: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 120 (%0.013:%0.11), avgs: 2 376: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 120 (%0.013:%0.11), avgs: 2 377: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 121 (%0.013:%0.11), avgs: 2 378: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 122 (%0.013:%0.12), avgs: 2 379: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 121 (%0.013:%0.12), avgs: 2 380: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 121 (%0.013:%0.12), avgs: 2 vertex spacing 3.87 +- 1.87 (0.02-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.03-->3.27) 381: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 122 (%0.013:%0.12), avgs: 2 382: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 121 (%0.013:%0.12), avgs: 2 383: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 122 (%0.013:%0.12), avgs: 2 384: dt: 0.09, sse: 4.9 (0.232, 21.2, 0.787), neg: 122 (%0.013:%0.12), avgs: 2 385: dt: 2.75, sse: 4.8 (0.232, 21.2, 0.787), neg: 120 (%0.013:%0.11), avgs: 2 vertex spacing 3.87 +- 1.87 (0.02-->20.57) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.03-->3.27) 386: dt: 1.01, sse: 4.8 (0.232, 21.1, 0.787), neg: 120 (%0.012:%0.12), avgs: 0 387: dt: 0.09, sse: 4.8 (0.232, 21.1, 0.787), neg: 121 (%0.012:%0.12), avgs: 0 vertex spacing 3.87 +- 1.87 (0.02-->20.57) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.27) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 388: dt: 386.18, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.11), avgs: 32 389: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.11), avgs: 32 390: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.11), avgs: 32 vertex spacing 3.88 +- 1.88 (0.02-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.27) 391: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.11), avgs: 32 392: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.11), avgs: 32 393: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 120 (%0.011:%0.11), avgs: 32 394: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 120 (%0.011:%0.11), avgs: 32 395: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 120 (%0.011:%0.11), avgs: 32 396: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.10), avgs: 32 397: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.10), avgs: 32 398: dt: 0.29, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.10), avgs: 32 399: dt: 15.23, sse: 1.0 (0.233, 21.2, 0.788), neg: 119 (%0.011:%0.10), avgs: 32 vertex spacing 3.88 +- 1.88 (0.02-->20.57) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.27) 400: dt: 38.51, sse: 0.9 (0.233, 21.2, 0.788), neg: 114 (%0.009:%0.10), avgs: 8 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.27) 401: dt: 7.44, sse: 0.9 (0.233, 21.2, 0.788), neg: 112 (%0.009:%0.09), avgs: 8 402: dt: 49.55, sse: 0.9 (0.233, 21.2, 0.788), neg: 111 (%0.009:%0.10), avgs: 8 403: dt: 5.88, sse: 0.8 (0.233, 21.2, 0.788), neg: 112 (%0.008:%0.10), avgs: 8 404: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 112 (%0.008:%0.10), avgs: 8 405: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 111 (%0.008:%0.09), avgs: 8 406: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 111 (%0.008:%0.09), avgs: 8 407: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 111 (%0.008:%0.09), avgs: 8 408: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 110 (%0.008:%0.09), avgs: 8 409: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 110 (%0.008:%0.09), avgs: 8 410: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 111 (%0.008:%0.10), avgs: 8 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 411: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 112 (%0.008:%0.10), avgs: 8 412: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 112 (%0.008:%0.10), avgs: 8 413: dt: 0.15, sse: 0.8 (0.233, 21.2, 0.788), neg: 112 (%0.008:%0.10), avgs: 8 414: dt: 18.87, sse: 0.8 (0.233, 21.2, 0.788), neg: 109 (%0.008:%0.09), avgs: 8 415: dt: 7.95, sse: 0.8 (0.233, 21.2, 0.788), neg: 110 (%0.008:%0.09), avgs: 8 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.28) 416: dt: 0.10, sse: 0.8 (0.233, 21.2, 0.788), neg: 110 (%0.008:%0.09), avgs: 2 417: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.008:%0.10), avgs: 2 418: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.008:%0.10), avgs: 2 419: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.008:%0.10), avgs: 2 420: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.008:%0.10), avgs: 2 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 421: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.008:%0.10), avgs: 2 422: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.008:%0.10), avgs: 2 423: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.008:%0.10), avgs: 2 424: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.007:%0.10), avgs: 2 425: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 113 (%0.007:%0.10), avgs: 2 426: dt: 0.09, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.007:%0.10), avgs: 2 427: dt: 2.17, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.007:%0.09), avgs: 2 428: dt: 0.82, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.007:%0.09), avgs: 2 429: dt: 0.28, sse: 0.8 (0.233, 21.2, 0.788), neg: 114 (%0.007:%0.09), avgs: 2 vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.28) 430: dt: 0.08, sse: 0.8 (0.233, 21.2, 0.788), neg: 115 (%0.007:%0.09), avgs: 0 vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.28) vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.28) tol=1.8e+01, host=vader, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 431: dt: 9.99, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.007:%0.09), avgs: 32 432: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.007:%0.09), avgs: 32 433: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.09), avgs: 32 434: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 114 (%0.006:%0.09), avgs: 32 435: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 114 (%0.006:%0.09), avgs: 32 436: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.09), avgs: 32 437: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 114 (%0.006:%0.09), avgs: 32 438: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.09), avgs: 32 439: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.09), avgs: 32 440: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 114 (%0.006:%0.09), avgs: 32 vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 441: dt: 0.29, sse: 0.4 (0.233, 21.2, 0.788), neg: 113 (%0.006:%0.09), avgs: 32 442: dt: 0.88, sse: 0.4 (0.233, 21.2, 0.788), neg: 113 (%0.006:%0.09), avgs: 32 vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1983 --> 1981) face area 0.32 +- 0.29 (-0.02-->3.28) 443: dt: 0.00, sse: 0.4 (0.233, 21.2, 0.788), neg: 113 (%0.006:%0.09), avgs: 8 444: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 114 (%0.006:%0.10), avgs: 8 445: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.10), avgs: 8 446: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.10), avgs: 8 447: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 115 (%0.006:%0.10), avgs: 8 448: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 116 (%0.006:%0.10), avgs: 8 449: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 116 (%0.006:%0.10), avgs: 8 450: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 116 (%0.006:%0.10), avgs: 8 vertex spacing 3.88 +- 1.88 (0.00-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 451: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 116 (%0.006:%0.10), avgs: 8 452: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 117 (%0.006:%0.10), avgs: 8 453: dt: 0.15, sse: 0.4 (0.233, 21.2, 0.788), neg: 117 (%0.006:%0.10), avgs: 8 454: dt: 12.49, sse: 0.4 (0.233, 21.3, 0.788), neg: 116 (%0.006:%0.09), avgs: 8 455: dt: 4.80, sse: 0.3 (0.233, 21.3, 0.788), neg: 118 (%0.006:%0.10), avgs: 8 456: dt: 0.50, sse: 0.3 (0.233, 21.3, 0.788), neg: 118 (%0.006:%0.10), avgs: 8 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 457: dt: 1.20, sse: 0.3 (0.233, 21.3, 0.788), neg: 115 (%0.006:%0.11), avgs: 2 458: dt: 0.56, sse: 0.3 (0.233, 21.3, 0.788), neg: 115 (%0.005:%0.10), avgs: 2 459: dt: 0.15, sse: 0.3 (0.233, 21.3, 0.788), neg: 116 (%0.005:%0.10), avgs: 2 460: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 118 (%0.005:%0.10), avgs: 2 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.02-->3.28) 461: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 119 (%0.005:%0.11), avgs: 2 462: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 119 (%0.005:%0.11), avgs: 2 463: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 116 (%0.005:%0.11), avgs: 2 464: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 120 (%0.006:%0.13), avgs: 2 465: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 119 (%0.006:%0.13), avgs: 2 466: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 119 (%0.006:%0.12), avgs: 2 467: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 117 (%0.005:%0.11), avgs: 2 468: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 116 (%0.005:%0.10), avgs: 2 469: dt: 0.09, sse: 0.3 (0.233, 21.3, 0.788), neg: 117 (%0.005:%0.11), avgs: 2 470: dt: 0.05, sse: 0.3 (0.233, 21.3, 0.788), neg: 117 (%0.005:%0.11), avgs: 2 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.01-->3.28) vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.01-->3.28) 471: dt: 0.00, sse: 0.3 (0.233, 21.3, 0.788), neg: 117 (%0.005:%0.11), avgs: 0 vertex spacing 3.88 +- 1.88 (0.01-->20.56) (max @ vno 1981 --> 1983) face area 0.32 +- 0.29 (-0.01-->3.28) 471: dt: 0.00, sse: 66.3 (0.233, 21.3, 0.788), neg: 117 (%0.005:%0.11), avgs: 32 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.01 hours with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.11/41 = 0.00275 epoch 3 (K=320.0), pass 1, starting sse = 0.99 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.21/43 = 0.00481 epoch 4 (K=1280.0), pass 1, starting sse = 0.39 integrating with navgs=32 and tol=3.200e+00 taking momentum steps... integrating with navgs=32 and tol=3.200e+00 integrating with navgs=32 and tol=3.200e+00 integrating with navgs=8 and tol=1.671e+00 taking momentum steps... integrating with navgs=8 and tol=1.671e+00 integrating with navgs=8 and tol=1.671e+00 integrating with navgs=2 and tol=9.648e-01 taking momentum steps... integrating with navgs=2 and tol=9.648e-01 integrating with navgs=2 and tol=9.648e-01 integrating with navgs=0 and tol=5.570e-01 pass 1 complete, delta sse/iter = 0.17/41 = 0.00419 final distance error %100000.00 optimization complete. unfolding took 0.01 hours #-------------------------------------------- #@# Fix Topology rh Wed Oct 17 01:32:44 CDT 2007 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga 990903_61167 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* 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 1.41.2.1 2007/01/05 16:58:33 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ before topology correction, eno=-6 (nv=8284, nf=16640, ne=24930, g=4) 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... 524 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 23 defects to be corrected 0 vertices coincident Computing Initial Surface Statistics -face loglikelihood: -8.4769 (-4.2385) -vertex loglikelihood: -8.2655 (-4.1328) -normal dot loglikelihood: -3.4290 (-3.4290) -quad curv loglikelihood: -6.1745 (-3.0873) Total Loglikelihood : -26.3460 CORRECTING DEFECT 0 (vertices=11, convex hull=42) l_mri = 1.00 l_unmri = 10.00 l_curv = 1.00 l_qcurv = 1.00 After retessellation of defect 0, euler #=-20 (7886,23262,15356) : difference with theory (-20) = 0 CORRECTING DEFECT 1 (vertices=29, convex hull=42) After retessellation of defect 1, euler #=-19 (7904,23334,15411) : difference with theory (-19) = 0 CORRECTING DEFECT 2 (vertices=9, convex hull=37) After retessellation of defect 2, euler #=-18 (7909,23362,15435) : difference with theory (-18) = 0 CORRECTING DEFECT 3 (vertices=11, convex hull=43) After retessellation of defect 3, euler #=-17 (7914,23391,15460) : difference with theory (-17) = 0 CORRECTING DEFECT 4 (vertices=32, convex hull=91) After retessellation of defect 4, euler #=-16 (7932,23489,15541) : difference with theory (-16) = 0 CORRECTING DEFECT 5 (vertices=7, convex hull=31) After retessellation of defect 5, euler #=-15 (7936,23508,15557) : difference with theory (-15) = 0 CORRECTING DEFECT 6 (vertices=30, convex hull=65) After retessellation of defect 6, euler #=-14 (7948,23565,15603) : difference with theory (-14) = 0 CORRECTING DEFECT 7 (vertices=16, convex hull=50) After retessellation of defect 7, euler #=-13 (7956,23608,15639) : difference with theory (-13) = 0 CORRECTING DEFECT 8 (vertices=13, convex hull=36) After retessellation of defect 8, euler #=-12 (7964,23645,15669) : difference with theory (-12) = 0 CORRECTING DEFECT 9 (vertices=10, convex hull=39) After retessellation of defect 9, euler #=-11 (7970,23675,15694) : difference with theory (-11) = 0 CORRECTING DEFECT 10 (vertices=23, convex hull=60) After retessellation of defect 10, euler #=-10 (7981,23735,15744) : difference with theory (-10) = 0 CORRECTING DEFECT 11 (vertices=12, convex hull=42) After retessellation of defect 11, euler #=-9 (7989,23779,15781) : difference with theory (-9) = 0 CORRECTING DEFECT 12 (vertices=7, convex hull=32) After retessellation of defect 12, euler #=-8 (7992,23795,15795) : difference with theory (-8) = 0 CORRECTING DEFECT 13 (vertices=18, convex hull=46) After retessellation of defect 13, euler #=-7 (8001,23839,15831) : difference with theory (-7) = 0 CORRECTING DEFECT 14 (vertices=7, convex hull=29) After retessellation of defect 14, euler #=-6 (8004,23855,15845) : difference with theory (-6) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=24) After retessellation of defect 15, euler #=-5 (8005,23863,15853) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=37, convex hull=67) After retessellation of defect 16, euler #=-4 (8022,23947,15921) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=5, convex hull=39) After retessellation of defect 17, euler #=-3 (8024,23963,15936) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=26, convex hull=62) After retessellation of defect 18, euler #=-2 (8036,24028,15990) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=17, convex hull=37) After retessellation of defect 19, euler #=-1 (8046,24070,16023) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=31, convex hull=48) After retessellation of defect 20, euler #=0 (8058,24125,16067) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=17, convex hull=55) After retessellation of defect 21, euler #=1 (8070,24181,16112) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=27, convex hull=61) After retessellation of defect 22, euler #=2 (8088,24258,16172) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.93 +- 0.24 (0.04-->3.04) (max @ vno 7694 --> 4904) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.93 +- 0.24 (0.04-->3.04) (max @ vno 7694 --> 4904) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 68 mutations (36.2%), 120 crossovers (63.8%), 12 vertices were eliminated building final representation... 196 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=8088, nf=16172, ne=24258, g=0) writing corrected surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 8.1 minutes reading input surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... 0 defective edges removing intersecting faces 000: 66 intersecting 001: 4 intersecting /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 64 intersecting 001: 7 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make Final Surf rh Wed Oct 17 01:40:52 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_make_surfaces -mgz -T1 brain.finalsurfs 990903_61167 rh INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.70.2.6 2007/01/09 19:15:32 nicks Exp $ $Id: mrisurf.c,v 1.441.2.5 2006/11/29 20:28:16 nicks Exp $ reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/filled.mgz... reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/brain.finalsurfs.mgz... reading volume /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri/wm.mgz... 10150 bright wm thresholded. 320 bright non-wm voxels segmented. reading original surface position from /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.orig... computing class statistics... border white: 20018 voxels (0.12%) border gray 17816 voxels (0.11%) WM: 100.7 +- 8.2 [70.0 --> 110.0] GM: 86.5 +- 18.1 [40.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 83.9 (was 70) setting MAX_BORDER_WHITE to 111.2 (was 105) setting MIN_BORDER_WHITE to 102.0 (was 85) setting MAX_CSF to 65.9 (was 40) setting MAX_GRAY to 94.8 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 93.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 47.8 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.85 +- 0.26 (0.01-->2.39) (max @ vno 6716 --> 6676) face area 0.31 +- 0.16 (0.00-->1.20) mean absolute distance = 2.37 +- 2.15 161 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=103, GM=102 using class modes intead of means.... mean inside = 98.9, mean outside = 83.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=104.5, 794 (794) missing vertices, mean dist -2.5 [2.6 (%85.7)->1.1 (%14.3))] %18 local maxima, %36 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=4, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.89 +- 0.30 (0.07-->2.89) (max @ vno 7694 --> 4904) face area 0.31 +- 0.18 (0.00-->1.94) vertex spacing 0.89 +- 0.34 (0.10-->3.30) (max @ vno 1029 --> 662) face area 0.31 +- 0.20 (0.00-->2.30) smoothing T1 volume with sigma = 1.000 vertex spacing 0.89 +- 0.34 (0.11-->3.33) (max @ vno 1029 --> 662) face area 0.31 +- 0.20 (0.00-->2.37) mean absolute distance = 0.91 +- 1.33 109 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=199800.0, rms=26.61 001: dt: 0.5000, sse=208363.7, rms=17.45 002: dt: 0.5000, sse=214966.7, rms=11.96 003: dt: 0.5000, sse=264464.3, rms=8.43 004: dt: 0.5000, sse=275603.4, rms=6.33 005: dt: 0.5000, sse=335274.1, rms=5.66 006: dt: 0.5000, sse=357845.0, rms=5.43 007: dt: 0.5000, sse=362779.2, rms=5.29 008: dt: 0.5000, sse=390836.1, rms=5.11 rms = 5.18, time step reduction 1 of 3 to 0.250... 009: dt: 0.2500, sse=367942.9, rms=5.04 rms = 5.04, time step reduction 2 of 3 to 0.125... 010: dt: 0.2500, sse=355295.8, rms=5.04 011: dt: 0.1250, sse=348555.8, rms=4.99 rms = 4.96, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=346488.9, rms=4.96 positioning took 0.7 minutes inhibiting deformation at non-cortical midline structures... mean border=104.4, 874 (406) missing vertices, mean dist -0.8 [1.4 (%60.6)->0.5 (%39.4))] %16 local maxima, %32 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=2, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.35 (0.07-->3.35) (max @ vno 7694 --> 4904) face area 0.31 +- 0.21 (0.00-->2.32) vertex spacing 0.89 +- 0.37 (0.10-->3.51) (max @ vno 1000 --> 1007) face area 0.31 +- 0.23 (0.00-->2.35) smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.37 (0.08-->3.56) (max @ vno 1000 --> 1007) face area 0.31 +- 0.23 (0.00-->2.38) mean absolute distance = 0.62 +- 1.09 118 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=313662.6, rms=5.75 013: dt: 0.5000, sse=379093.3, rms=5.52 014: dt: 0.5000, sse=405696.1, rms=5.30 015: dt: 0.5000, sse=417340.1, rms=4.77 016: dt: 0.5000, sse=424668.1, rms=4.56 017: dt: 0.5000, sse=429853.8, rms=4.28 rms = 4.28, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=402008.4, rms=4.18 019: dt: 0.2500, sse=384139.6, rms=4.11 020: dt: 0.2500, sse=376288.7, rms=4.04 rms = 4.00, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=369885.1, rms=4.00 rms = 3.96, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=362383.7, rms=3.96 positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... mean border=104.5, 959 (279) missing vertices, mean dist -0.6 [1.1 (%56.7)->0.3 (%43.3))] %21 local maxima, %24 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=1, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.36 (0.09-->3.56) (max @ vno 1000 --> 1007) face area 0.31 +- 0.23 (0.00-->2.42) mean absolute distance = 0.49 +- 0.85 102 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=349749.7, rms=4.10 rms = 4.17, time step reduction 1 of 3 to 0.250... rms = 4.07, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=347394.1, rms=4.07 rms = 4.07, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=347394.1, rms=4.07 positioning took 0.1 minutes inhibiting deformation at non-cortical midline structures... mean border=104.6, 1089 (270) missing vertices, mean dist -0.5 [0.9 (%56.5)->0.3 (%43.5))] %22 local maxima, %20 large gradients and % 2 min vals, 0 gradients ignored tol=1.0e-04, host=vader, nav=0, nbrs=2, l_repulse=1.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.36 (0.05-->3.60) (max @ vno 1000 --> 1007) face area 0.31 +- 0.23 (0.00-->2.46) writing white matter surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.white... writing smoothed curvature to rh.curv writing smoothed area to rh.area vertex spacing 0.89 +- 0.36 (0.15-->3.65) (max @ vno 1000 --> 1007) face area 0.31 +- 0.23 (0.00-->2.58) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=346861.2, rms=4.11 025: dt: 0.5000, sse=524065.0, rms=3.84 rms = 3.94, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=488764.2, rms=3.72 rms = 3.69, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=470504.6, rms=3.69 028: dt: 0.1250, sse=460659.7, rms=3.59 rms = 3.55, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=463469.2, rms=3.55 positioning took 0.3 minutes generating cortex label... writing cortex label to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/label/rh.cortex.label... LabelWrite: saving to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/label/rh.cortex.label writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.curv writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.area smoothing surface for 5 iterations... mean border=78.3, 996 (996) missing vertices, mean dist 3.0 [0.3 (%0.1)->3.2 (%99.9))] %17 local maxima, %15 large gradients and %14 min vals, 16 gradients ignored tol=1.0e-04, host=vader, 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 vertex spacing 0.87 +- 0.39 (0.11-->4.37) (max @ vno 266 --> 267) face area 0.28 +- 0.22 (0.00-->3.08) vertex spacing 0.93 +- 0.44 (0.08-->4.79) (max @ vno 5618 --> 5619) face area 0.28 +- 0.23 (0.00-->3.49) vertex spacing 0.96 +- 0.48 (0.07-->5.30) (max @ vno 5618 --> 5619) face area 0.28 +- 0.24 (0.00-->3.77) vertex spacing 0.95 +- 0.49 (0.08-->5.63) (max @ vno 163 --> 229) face area 0.28 +- 0.25 (0.00-->3.75) vertex spacing 0.95 +- 0.50 (0.09-->6.72) (max @ vno 163 --> 229) face area 0.28 +- 0.25 (0.00-->3.77) smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=162391.8, rms=26.09 001: dt: 0.5000, sse=166181.5, rms=25.13 002: dt: 0.5000, sse=171018.3, rms=23.73 003: dt: 0.5000, sse=189881.4, rms=22.42 004: dt: 0.5000, sse=229260.5, rms=21.06 005: dt: 0.5000, sse=275935.5, rms=19.59 006: dt: 0.5000, sse=293536.3, rms=18.13 007: dt: 0.5000, sse=309600.2, rms=16.91 008: dt: 0.5000, sse=320546.6, rms=15.99 009: dt: 0.5000, sse=313286.1, rms=14.99 010: dt: 0.5000, sse=321891.3, rms=14.08 011: dt: 0.5000, sse=338463.2, rms=12.73 012: dt: 0.5000, sse=342206.8, rms=12.08 013: dt: 0.5000, sse=350535.4, rms=11.35 014: dt: 0.5000, sse=346324.2, rms=11.12 015: dt: 0.5000, sse=344259.5, rms=10.81 rms = 10.77, time step reduction 1 of 3 to 0.250... 016: dt: 0.5000, sse=338098.3, rms=10.77 017: dt: 0.2500, sse=273069.5, rms=9.72 rms = 9.75, time step reduction 2 of 3 to 0.125... 018: dt: 0.1250, sse=256914.6, rms=9.35 019: dt: 0.1250, sse=239105.4, rms=9.19 020: dt: 0.1250, sse=226616.8, rms=8.72 021: dt: 0.1250, sse=223385.0, rms=8.65 022: dt: 0.1250, sse=218581.5, rms=8.53 023: dt: 0.1250, sse=219792.0, rms=8.46 024: dt: 0.1250, sse=222927.4, rms=8.40 rms = 8.42, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=222927.4, rms=8.40 positioning took 1.3 minutes mean border=79.4, 1170 (593) missing vertices, mean dist 0.5 [0.2 (%67.8)->1.9 (%32.2))] %17 local maxima, %14 large gradients and %13 min vals, 15 gradients ignored tol=1.0e-04, host=vader, 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=235252.2, rms=9.74 rms = 10.50, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=233636.6, rms=9.07 rms = 9.24, time step reduction 2 of 3 to 0.125... 027: dt: 0.1250, sse=229671.1, rms=8.92 028: dt: 0.1250, sse=227366.1, rms=8.76 rms = 8.80, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=227366.1, rms=8.76 positioning took 0.2 minutes mean border=81.2, 1246 (546) missing vertices, mean dist 0.3 [0.2 (%69.3)->1.2 (%30.7))] %15 local maxima, %16 large gradients and %12 min vals, 14 gradients ignored tol=1.0e-04, host=vader, 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 vertex spacing 0.95 +- 0.49 (0.12-->6.26) (max @ vno 163 --> 229) face area 0.36 +- 0.32 (0.00-->4.91) smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=228312.4, rms=9.02 rms = 10.20, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=230708.0, rms=8.60 rms = 8.61, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=229495.5, rms=8.49 032: dt: 0.1250, sse=236274.7, rms=8.30 rms = 8.36, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=236274.7, rms=8.30 positioning took 0.2 minutes mean border=81.5, 1405 (533) missing vertices, mean dist 0.1 [0.2 (%67.7)->0.7 (%32.3))] %15 local maxima, %15 large gradients and %11 min vals, 16 gradients ignored tol=1.0e-04, host=vader, 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 vertex spacing 0.95 +- 0.49 (0.16-->6.04) (max @ vno 162 --> 112) face area 0.36 +- 0.32 (0.00-->4.80) writing pial surface to /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.pial... writing smoothed curvature to rh.curv.pial writing smoothed area to rh.area.pial vertex spacing 0.95 +- 0.50 (0.17-->5.90) (max @ vno 163 --> 229) face area 0.36 +- 0.32 (0.00-->4.80) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. positioning took 6.4 minutes 000: dt: 0.0000, sse=236973.8, rms=8.51 rms = 9.78, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=242593.2, rms=8.26 rms = 8.48, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=241305.7, rms=8.18 036: dt: 0.1250, sse=251775.3, rms=8.12 rms = 8.21, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=251775.3, rms=8.12 positioning took 0.2 minutes writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.curv.pial writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.area.pial 0 of 8088 vertices processed 0 of 8088 vertices processed thickness calculation complete, 3:1 truncations. 1586 vertices at 0 distance 3309 vertices at 1 distance 2674 vertices at 2 distance 1169 vertices at 3 distance 461 vertices at 4 distance 163 vertices at 5 distance 54 vertices at 6 distance 33 vertices at 7 distance 20 vertices at 8 distance 11 vertices at 9 distance 2 vertices at 10 distance 3 vertices at 11 distance 1 vertices at 12 distance 0 vertices at 13 distance 0 vertices at 14 distance 0 vertices at 15 distance 0 vertices at 16 distance 0 vertices at 17 distance 0 vertices at 18 distance 0 vertices at 19 distance 0 vertices at 20 distance writing curvature file /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.thickness #-------------------------------------------- #@# Smooth2 rh Wed Oct 17 01:47:14 CDT 2007 mris_smooth -n 3 -nw ../surf/rh.white ../surf/rh.smoothwm /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts smoothing for 3 iterations smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Wed Oct 17 01:47:14 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 21.0 mm, total surface area = 4353 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation took 0.1 minutes step 000: RMS=0.164 (target=0.015) step 005: RMS=0.119 (target=0.015) step 010: RMS=0.106 (target=0.015) step 015: RMS=0.095 (target=0.015) step 020: RMS=0.087 (target=0.015) step 025: RMS=0.082 (target=0.015) step 030: RMS=0.079 (target=0.015) step 035: RMS=0.073 (target=0.015) step 040: RMS=0.072 (target=0.015) step 045: RMS=0.072 (target=0.015) step 050: RMS=0.071 (target=0.015) step 055: RMS=0.071 (target=0.015) step 060: RMS=0.071 (target=0.015) inflation complete. #-------------------------------------------- #@# Cortical ribbon mask rh Wed Oct 17 01:47:19 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/mri mri_surf2vol --mkmask --hemi rh --fillribbon --template orig.mgz --volregidentity 990903_61167 --outvol rh.ribbon.mgz gdiagno = -1 Using identity matrix for registration Qa2v: SurfXYZ to VolCRS: ------------------------------ -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; -------------------------------------------------- subjects dir /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE hemi rh mksurfmask 1 projfrac 0 volreg file (null) outvol path rh.ribbon.mgz template path orig.mgz ------- Anat2Vol Registration (TkReg)---- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ----------------------------------------- height = 256 width = 256 depth = 256 xsize = 1.000000 ysize = 1.000000 zsize = 1.000000 cdc = -1.000000 0.000000 0.000000 rdc = 0.000000 0.000000 -1.000000 sdc = 0.000000 1.000000 0.000000 xyz0 = 0.000000 0.000000 0.000000 Gdiag_no -1 Reading surface /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.white Done reading source surface Reading thickness /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/990903_61167/surf/rh.thickness Done surf nframes = 1 INFO: mapping vertices to closest voxel INFO: resampling surface to volume at projfrac=0.00, 4614 hits INFO: resampling surface to volume at projfrac=0.05, 4646 hits INFO: resampling surface to volume at projfrac=0.10, 4685 hits INFO: resampling surface to volume at projfrac=0.15, 4721 hits INFO: resampling surface to volume at projfrac=0.20, 4733 hits INFO: resampling surface to volume at projfrac=0.25, 4703 hits INFO: resampling surface to volume at projfrac=0.30, 4677 hits INFO: resampling surface to volume at projfrac=0.35, 4711 hits INFO: resampling surface to volume at projfrac=0.40, 4711 hits INFO: resampling surface to volume at projfrac=0.45, 4702 hits INFO: resampling surface to volume at projfrac=0.50, 4732 hits INFO: resampling surface to volume at projfrac=0.55, 4725 hits INFO: resampling surface to volume at projfrac=0.60, 4721 hits INFO: resampling surface to volume at projfrac=0.65, 4676 hits INFO: resampling surface to volume at projfrac=0.70, 4679 hits INFO: resampling surface to volume at projfrac=0.75, 4686 hits INFO: resampling surface to volume at projfrac=0.80, 4662 hits INFO: resampling surface to volume at projfrac=0.85, 4709 hits INFO: resampling surface to volume at projfrac=0.90, 4716 hits INFO: resampling surface to volume at projfrac=0.95, 4744 hits INFO: writing output volume to rh.ribbon.mgz done #------------------------------------------ recon-all finished without error at Wed Oct 17 01:48:13 CDT 2007