Fri Jun 19 12:20:27 CEST 2009 /data/MOODS2/freesurfer/1005 /usr/local/freesurfer/bin/recon-all -i /data/MOODS2/1005/MPRage/1005_mpr_t1_1st.nii -i /data/MOODS2/1005/MPRage/1005_mpr_t1_2nd.nii -i /data/MOODS2/1005/MPRage/1005_mpr_t1_3rd.nii -subjid 1005 subjid 1005 setenv SUBJECTS_DIR /data/MOODS2/freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Linux impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 6842584 kbytes vmemoryuse 8123680 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 70656 total used free shared buffers cached Mem: 8050076 3609292 4440784 0 64172 1864512 Swap: 2104472 0 2104472 ######################################## program versions used $Id: recon-all,v 1.133.2.30 2008/04/17 20:38:23 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $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: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_em_register.c,v 1.57.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_label.c,v 1.80.2.4 2008/03/26 19:43:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_make_surfaces.c,v 1.99.2.3 2008/01/07 22:30:43 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.1 2007/12/19 01:22:05 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-10:20:27-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_1st.nii /data/MOODS2/freesurfer/1005/mri/orig/001.mgz mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_1st.nii /data/MOODS2/freesurfer/1005/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/1005/MPRage/1005_mpr_t1_1st.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/orig/001.mgz... /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_2nd.nii /data/MOODS2/freesurfer/1005/mri/orig/002.mgz mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_2nd.nii /data/MOODS2/freesurfer/1005/mri/orig/002.mgz $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/1005/MPRage/1005_mpr_t1_2nd.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0174814, -0.995733, 0.0906118) j_ras = (0.133542, 0.0921389, 0.986751) k_ras = (0.990889, 0.00514928, -0.134583) writing to /data/MOODS2/freesurfer/1005/mri/orig/002.mgz... /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_3rd.nii /data/MOODS2/freesurfer/1005/mri/orig/003.mgz mri_convert /data/MOODS2/1005/MPRage/1005_mpr_t1_3rd.nii /data/MOODS2/freesurfer/1005/mri/orig/003.mgz $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/1005/MPRage/1005_mpr_t1_3rd.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.023198, -0.995392, 0.0930422) j_ras = (0.138037, 0.0953649, 0.985825) k_ras = (0.990156, 0.010026, -0.139613) writing to /data/MOODS2/freesurfer/1005/mri/orig/003.mgz... #------------------------------------------ recon-all finished without error at Fri Jun 19 12:21:01 CEST 2009 New invocation of recon-all Fri Jun 19 13:12:09 CEST 2009 /data/MOODS2/freesurfer/1005 /usr/local/freesurfer/bin/recon-all -subjid 1005 -all subjid 1005 setenv SUBJECTS_DIR /data/MOODS2/freesurfer FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Linux impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 6842584 kbytes vmemoryuse 8123680 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 70656 total used free shared buffers cached Mem: 8050076 5587844 2462232 0 64568 3895884 Swap: 2104472 0 2104472 ######################################## program versions used $Id: recon-all,v 1.133.2.30 2008/04/17 20:38:23 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.4.2b $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: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_watershed.cpp,v 1.67.2.4 2007/11/18 22:52:02 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_em_register.c,v 1.57.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_normalize.c,v 1.38.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_register.c,v 1.63.2.1 2008/03/02 02:00:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_ca_label.c,v 1.80.2.4 2008/03/26 19:43:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_concatenate_lta.c,v 1.3 2007/05/17 19:56:59 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_make_surfaces.c,v 1.99.2.3 2008/01/07 22:30:43 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.1 2007/12/19 01:22:05 nicks Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/06/19-11:12:09-GMT BuildTimeStamp: Jun 14 2008 07:28:57 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: fmrt Machine: impsy-pc4 Platform: Linux PlatformVersion: 2.6.27.19-3.2-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2007-06-20.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Jun 19 13:12:09 CEST 2009 Found 3 runs /data/MOODS2/freesurfer/1005/mri/orig/001.mgz /data/MOODS2/freesurfer/1005/mri/orig/002.mgz /data/MOODS2/freesurfer/1005/mri/orig/003.mgz /data/MOODS2/freesurfer/1005 mri_motion_correct.fsl -o /data/MOODS2/freesurfer/1005/mri/rawavg.mgz -wild /data/MOODS2/freesurfer/1005/mri/orig/001.mgz /data/MOODS2/freesurfer/1005/mri/orig/002.mgz /data/MOODS2/freesurfer/1005/mri/orig/003.mgz tmpdir is /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /data/MOODS2/freesurfer/1005/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /data/MOODS2/freesurfer/1005/mri/orig/001.mgz Fri Jun 19 13:12:30 CEST 2009 /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/orig/001.mgz /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/orig/001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img... Analyze Output Matrix -0.014 0.098 0.995 -99.260; -0.999 -0.034 -0.011 150.729; -0.033 0.995 -0.099 -122.297; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /data/MOODS2/freesurfer/1005/mri/orig/002.mgz Fri Jun 19 13:12:33 CEST 2009 /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/orig/002.mgz /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/orig/002.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0174814, -0.995733, 0.0906118) j_ras = (0.133542, 0.0921389, 0.986751) k_ras = (0.990889, 0.00514928, -0.134583) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img... Analyze Output Matrix 0.017 0.134 0.991 -109.797; -0.996 0.092 0.005 111.700; 0.091 0.987 -0.135 -147.576; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /data/MOODS2/freesurfer/1005/mri/orig/003.mgz Fri Jun 19 13:12:36 CEST 2009 /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/orig/003.mgz /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img -odt float $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/orig/003.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.023198, -0.995392, 0.0930422) j_ras = (0.138037, 0.0953649, 0.985825) k_ras = (0.990156, 0.010026, -0.139613) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img... Analyze Output Matrix 0.023 0.138 0.990 -111.320; -0.995 0.095 0.010 110.941; 0.093 0.986 -0.140 -147.198; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img Fri Jun 19 13:12:39 CEST 2009 /data/MOODS2/freesurfer/1005 fsl_rigid_register -maxangle 90 -r /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img -i /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img -o /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img -tmpdir /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130 -cleanup $Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $ Fri Jun 19 13:12:39 CEST 2009 /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii... -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0174814, -0.995733, 0.0906118) j_ras = (0.133542, 0.0921389, 0.986751) k_ras = (0.990889, 0.00514928, -0.134583) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii... -------------------------------------- /data/MOODS2/freesurfer/1005 tkregister2_cmdl --targ /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img --mov /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img --reg /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat --fslregout /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img movable volume /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img reg file /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 INFO: loading target /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -88.001; 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) -------- -0.017 0.996 -0.091 19.467; 0.991 0.005 -0.135 0.545; -0.134 -0.092 -0.987 -15.557; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.017 0.996 -0.091 19.467; 0.991 0.005 -0.135 0.545; -0.134 -0.092 -0.987 -15.557; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- 0.992 -0.019 0.126 19.467; 0.015 0.999 0.037 0.545; -0.127 -0.034 0.991 -15.557; 0.000 0.000 0.000 1.000; register: file /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1.00001, ref det = -0.999985 Init FSL Mat based on geometry ------------------- 0.99183977 -0.12663057 -0.01479381 39.84098434 0.12602341 0.99135381 -0.03654784 -24.75749016 0.01929406 0.03438515 0.99922246 -7.50833941 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /data/MOODS2/freesurfer/1005 calling eval flirt -in /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.hdr -out /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.hdr -init /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/initxfm.fslmat -omat /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.fslmat -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img... Analyze Output Matrix -0.014 0.098 0.995 -99.260; -0.999 -0.034 -0.011 150.729; -0.033 0.995 -0.099 -122.297; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Fri Jun 19 13:12:39 CEST 2009 Ended at Fri Jun 19 13:14:46 CEST 2009 fsl_rigid_register Done To check results, run: tkmedit -f /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img -aux /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img mv /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img ----------------------------------------- Motion Correcting /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img Fri Jun 19 13:14:46 CEST 2009 /data/MOODS2/freesurfer/1005 fsl_rigid_register -maxangle 90 -r /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img -i /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img -o /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img -tmpdir /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130 -cleanup $Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $ Fri Jun 19 13:14:46 CEST 2009 /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.nii... -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.023198, -0.995392, 0.0930422) j_ras = (0.138037, 0.0953649, 0.985825) k_ras = (0.990156, 0.010026, -0.139613) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.nii... -------------------------------------- /data/MOODS2/freesurfer/1005 tkregister2_cmdl --targ /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img --mov /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img --reg /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat --fslregout /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/initxfm.fslmat --regheader --noedit --s doesnotmatter target volume /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img movable volume /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img reg file /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 INFO: loading target /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -88.001; 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) -------- -0.023 0.995 -0.093 19.284; 0.990 0.010 -0.140 0.862; -0.138 -0.095 -0.986 -15.524; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.023 0.995 -0.093 19.284; 0.990 0.010 -0.140 0.862; -0.138 -0.095 -0.986 -15.524; 0.000 0.000 0.000 1.000; subject = doesnotmatter RegMat --------------------------- 0.991 -0.025 0.129 19.284; 0.019 0.999 0.042 0.862; -0.130 -0.039 0.991 -15.524; 0.000 0.000 0.000 1.000; register: file /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1.00001, ref det = -0.999985 Init FSL Mat based on geometry ------------------- 0.99133706 -0.12988785 -0.01949046 40.60005951 0.12899122 0.99076468 -0.04178929 -24.50853157 0.02473840 0.03891334 0.99893659 -9.04349422 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /data/MOODS2/freesurfer/1005 calling eval flirt -in /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/invol.fsl_rigid_register.hdr -out /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/refvol.fsl_rigid_register.hdr -init /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/initxfm.fslmat -omat /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.fslmat -------------------------------------- /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img... Analyze Output Matrix -0.014 0.098 0.995 -99.260; -0.999 -0.034 -0.011 150.729; -0.033 0.995 -0.099 -122.297; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Fri Jun 19 13:14:46 CEST 2009 Ended at Fri Jun 19 13:16:59 CEST 2009 fsl_rigid_register Done To check results, run: tkmedit -f /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img -aux /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img mv /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/resampled.img /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img ----------------------------------------- Averaging Fri Jun 19 13:16:59 CEST 2009 /data/MOODS2/freesurfer/1005 inhibiting isotropic volume interpolation 1 of 3: reading /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-1.img... 2 of 3: reading /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-2.img... 3 of 3: reading /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/cor-3.img... writing to /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/avgvol.img... Analyze Output Matrix -0.014 0.098 0.995 -99.260; -0.999 -0.034 -0.011 150.729; -0.033 0.995 -0.099 -122.297; 0.000 0.000 0.000 1.000; alignment and averaging took 0 minutes and 15 seconds. -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting Average to output Fri Jun 19 13:17:14 CEST 2009 /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/avgvol.img /data/MOODS2/freesurfer/1005/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0 mri_convert /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/avgvol.img /data/MOODS2/freesurfer/1005/mri/rawavg.mgz -tr 0 -te 0 -TI 0 -flip_angle 0 $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/tmp-mri_motion_correct.fsl-18130/avgvol.img... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) writing to /data/MOODS2/freesurfer/1005/mri/rawavg.mgz... ----------------------------------------- Started at: Fri Jun 19 13:12:17 CEST 2009 Ended at: Fri Jun 19 13:17:23 CEST 2009 mri_motion_correct.fsl: done /data/MOODS2/freesurfer/1005 mri_convert /data/MOODS2/freesurfer/1005/mri/rawavg.mgz /data/MOODS2/freesurfer/1005/mri/orig.mgz --conform mri_convert /data/MOODS2/freesurfer/1005/mri/rawavg.mgz /data/MOODS2/freesurfer/1005/mri/orig.mgz --conform $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from /data/MOODS2/freesurfer/1005/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.0142309, -0.999351, -0.0330895) j_ras = (0.0983761, -0.0343316, 0.994557) k_ras = (0.995048, -0.0108982, -0.0988008) Original Data has (1, 1, 0.999985) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 3 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data/MOODS2/freesurfer/1005/mri/orig.mgz... mri_add_xform_to_header -c /data/MOODS2/freesurfer/1005/mri/transforms/talairach.xfm /data/MOODS2/freesurfer/1005/mri/orig.mgz /data/MOODS2/freesurfer/1005/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Jun 19 13:17:38 CEST 2009 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /data/MOODS2/freesurfer/1005/mri /usr/local/freesurfer/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 impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux Fri Jun 19 13:17:38 CEST 2009 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 tmpdir is ./tmp.mri_nu_correct.mni.20481 /data/MOODS2/freesurfer/1005/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20481/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20481/nu0.mnc $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.86733e-08, 1.19209e-07) j_ras = (1.11759e-07, -3.49246e-09, -1) k_ras = (5.12227e-08, 1, 9.31323e-10) writing to ./tmp.mri_nu_correct.mni.20481/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Jun 19 13:17:43 CEST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.20481/nu0.mnc ./tmp.mri_nu_correct.mni.20481/nu1.mnc [fmrt@impsy-pc4:/data/MOODS2/freesurfer/1005/mri/] [2009-06-19 13:17:43] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /tmp/nu_correct_20582/ ./tmp.mri_nu_correct.mni.20481/nu0.mnc ./tmp.mri_nu_correct.mni.20481/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: 0.00129219 [fmrt@impsy-pc4:/data/MOODS2/freesurfer/1005/mri/] [2009-06-19 13:18:39] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20481/nu0.mnc /tmp/nu_correct_20582//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 Fri Jun 19 13:18:43 CEST 2009 nu_correct -clobber ./tmp.mri_nu_correct.mni.20481/nu1.mnc ./tmp.mri_nu_correct.mni.20481/nu2.mnc [fmrt@impsy-pc4:/data/MOODS2/freesurfer/1005/mri/] [2009-06-19 13:18:43] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /tmp/nu_correct_21869/ ./tmp.mri_nu_correct.mni.20481/nu1.mnc ./tmp.mri_nu_correct.mni.20481/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() Number of iterations: 25 CV of field change: 0.000966871 [fmrt@impsy-pc4:/data/MOODS2/freesurfer/1005/mri/] [2009-06-19 13:19:12] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20481/nu1.mnc /tmp/nu_correct_21869//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.20481/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20481/nu2.mnc nu.mgz --like orig.mgz WARNING: --like does not work on multi-frame data $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from ./tmp.mri_nu_correct.mni.20481/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.86733e-08, 1.19209e-07) j_ras = (1.11759e-07, -3.49246e-09, -1) k_ras = (5.12227e-08, 1, 9.31323e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Fri Jun 19 13:19:24 CEST 2009 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Fri Jun 19 13:19:24 CEST 2009 /data/MOODS2/freesurfer/1005/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm /data/MOODS2/freesurfer/1005/mri /usr/local/freesurfer/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 impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux Fri Jun 19 13:19:24 CEST 2009 -------------------------------------------- mri_convert nu.mgz talsrcimg.img $Id: mri_convert.c,v 1.146.2.2 2008/03/02 02:53:20 nicks Exp $ reading from nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -5.86733e-08, 1.19209e-07) j_ras = (1.11759e-07, -3.49246e-09, -1) k_ras = (5.12227e-08, 1, 9.31323e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 0.000 0.000 129.152; -0.000 -0.000 1.000 -112.586; 0.000 -1.000 0.000 121.939; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------------- mpr2mni305 talsrcimg Fri Jun 19 13:19:27 CEST 2009 /usr/local/freesurfer/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 $ Fri Jun 19 13:19:29 2009 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 $ Fri Jun 19 13:19:54 2009 Writing: talsrcimg_g11.4dfp.hdr Writing: talsrcimg_g11.4dfp.ifh including: talsrcimg.4dfp.img.rec in talsrcimg_g11.4dfp.img.rec --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/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 $ /usr/local/freesurfer/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: /usr/local/freesurfer/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 -45.0000 9655.3447 10.4764 0.0000 -45.0000 -45.0000 9974.9326 10.4879 7.5000 -45.0000 -45.0000 9521.8281 10.5001 -7.5000 -37.5000 -45.0000 9914.8428 10.4926 0.0000 -37.5000 -45.000010245.8594 10.5050 7.5000 -37.5000 -45.0000 9754.6543 10.5228 -7.5000 -30.0000 -45.000010437.9854 10.4285 0.0000 -30.0000 -45.000010795.6260 10.4409 7.5000 -30.0000 -45.000010262.1924 10.4601 -7.5000 -22.5000 -45.000010943.0332 10.3923 0.0000 -22.5000 -45.000011333.3047 10.4039 7.5000 -22.5000 -45.000010759.9092 10.4181 -7.5000 -15.0000 -45.000011353.0283 10.3639 0.0000 -15.0000 -45.000011777.4355 10.3743 7.5000 -15.0000 -45.000011185.0752 10.3823 -7.5000 -7.5000 -45.000011661.4521 10.3405 0.0000 -7.5000 -45.000012090.9316 10.3507 7.5000 -7.5000 -45.000011496.4570 10.3577 -7.5000 0.0000 -45.000011873.5586 10.3311 0.0000 0.0000 -45.000012333.5391 10.3423 7.5000 0.0000 -45.000011739.1064 10.3542 -7.5000 7.5000 -45.000011208.6885 10.4473 0.0000 7.5000 -45.000011654.5869 10.4595 7.5000 7.5000 -45.000011074.6416 10.4773 -7.5000 15.0000 -45.000010547.7109 10.7233 0.0000 15.0000 -45.000010953.4902 10.7352 7.5000 15.0000 -45.000010396.0732 10.7548 -7.5000 22.5000 -45.0000 9882.7754 11.0573 0.0000 22.5000 -45.000010275.8145 11.0665 7.5000 22.5000 -45.0000 9751.4951 11.0817 -7.5000 30.0000 -45.0000 9296.1367 11.2680 0.0000 30.0000 -45.0000 9660.2998 11.2775 7.5000 30.0000 -45.0000 9181.9238 11.2869 -7.5000 37.5000 -45.0000 8983.7129 11.6383 0.0000 37.5000 -45.0000 9350.3486 11.6478 7.5000 37.5000 -45.0000 8908.7930 11.6575 -7.5000 45.0000 -45.0000 8343.1211 11.7499 0.0000 45.0000 -45.0000 8706.7979 11.7632 7.5000 45.0000 -45.0000 8290.7080 11.7790 -7.5000 -45.0000 -37.500010259.7109 10.4196 0.0000 -45.0000 -37.500010608.4395 10.4254 7.5000 -45.0000 -37.500010098.1289 10.4320 -7.5000 -37.5000 -37.500010541.2793 10.4376 0.0000 -37.5000 -37.500010906.4326 10.4448 7.5000 -37.5000 -37.500010355.8086 10.4571 -7.5000 -30.0000 -37.500011093.2539 10.3741 0.0000 -30.0000 -37.500011471.3838 10.3827 7.5000 -30.0000 -37.500010883.4893 10.3987 -7.5000 -22.5000 -37.500011623.8906 10.3378 0.0000 -22.5000 -37.500012032.4238 10.3463 7.5000 -22.5000 -37.500011405.3359 10.3596 -7.5000 -15.0000 -37.500012063.3564 10.3092 0.0000 -15.0000 -37.500012506.6445 10.3158 7.5000 -15.0000 -37.500011847.4893 10.3228 -7.5000 -7.5000 -37.500012396.2598 10.2853 0.0000 -7.5000 -37.500012844.6201 10.2905 7.5000 -7.5000 -37.500012171.8789 10.2944 -7.5000 0.0000 -37.500012626.3936 10.2765 0.0000 0.0000 -37.500013106.0947 10.2821 7.5000 0.0000 -37.500012397.5361 10.2888 -7.5000 7.5000 -37.500011899.4209 10.3935 0.0000 7.5000 -37.500012340.6475 10.4006 7.5000 7.5000 -37.500011687.3242 10.4129 -7.5000 15.0000 -37.500011171.4121 10.6693 0.0000 15.0000 -37.500011571.4238 10.6782 7.5000 15.0000 -37.500010944.4072 10.6945 -7.5000 22.5000 -37.500010464.5127 10.9996 0.0000 22.5000 -37.500010851.6660 11.0066 7.5000 22.5000 -37.500010267.8818 11.0213 -7.5000 30.0000 -37.5000 9830.1797 11.2069 0.0000 30.0000 -37.500010196.5205 11.2136 7.5000 30.0000 -37.5000 9676.7422 11.2228 -7.5000 37.5000 -37.5000 9479.0986 11.5733 0.0000 37.5000 -37.5000 9868.5879 11.5786 7.5000 37.5000 -37.5000 9368.1934 11.5859 -7.5000 45.0000 -37.5000 8785.4053 11.6831 0.0000 45.0000 -37.5000 9174.7500 11.6922 7.5000 45.0000 -37.5000 8711.1963 11.7031 -7.5000 -45.0000 -30.000011068.1514 10.8416 0.0000 -45.0000 -30.000011456.2061 10.8408 7.5000 -45.0000 -30.000010862.6367 10.8462 -7.5000 -37.5000 -30.000011370.6777 10.8607 0.0000 -37.5000 -30.000011768.5088 10.8620 7.5000 -37.5000 -30.000011146.3594 10.8743 -7.5000 -30.0000 -30.000011955.8662 10.7912 0.0000 -30.0000 -30.000012371.9385 10.7957 7.5000 -30.0000 -30.000011721.9707 10.8133 -7.5000 -22.5000 -30.000012515.6865 10.7502 0.0000 -22.5000 -30.000012953.8916 10.7554 7.5000 -22.5000 -30.000012270.6904 10.7708 -7.5000 -15.0000 -30.000012999.5225 10.7199 0.0000 -15.0000 -30.000013471.3232 10.7226 7.5000 -15.0000 -30.000012751.0850 10.7305 -7.5000 -7.5000 -30.000013369.9219 10.6977 0.0000 -7.5000 -30.000013857.7402 10.6974 7.5000 -7.5000 -30.000013116.7686 10.7006 -7.5000 0.0000 -30.000013627.7666 10.6917 0.0000 0.0000 -30.000014132.6250 10.6910 7.5000 0.0000 -30.000013347.1904 10.6965 -7.5000 7.5000 -30.000012810.0469 10.8141 0.0000 7.5000 -30.000013274.1807 10.8154 7.5000 7.5000 -30.000012545.8574 10.8277 -7.5000 15.0000 -30.000012007.2188 11.0998 0.0000 15.0000 -30.000012434.5664 11.1047 7.5000 15.0000 -30.000011735.7500 11.1223 -7.5000 22.5000 -30.000011229.2773 11.4385 0.0000 22.5000 -30.000011637.8438 11.4425 7.5000 22.5000 -30.000011004.1631 11.4596 -7.5000 30.0000 -30.000010500.9912 11.6553 0.0000 30.0000 -30.000010911.4766 11.6584 7.5000 30.0000 -30.000010351.7119 11.6696 -7.5000 37.5000 -30.000010116.3076 12.0387 0.0000 37.5000 -30.000010552.0195 12.0391 7.5000 37.5000 -30.000010016.0566 12.0475 -7.5000 45.0000 -30.0000 9376.9053 12.1641 0.0000 45.0000 -30.0000 9813.8818 12.1673 7.5000 45.0000 -30.0000 9313.0439 12.1792 -7.5000 -45.0000 -22.500011852.7334 11.2190 0.0000 -45.0000 -22.500012276.5859 11.2187 7.5000 -45.0000 -22.500011634.9141 11.2297 -7.5000 -37.5000 -22.500012163.4512 11.2363 0.0000 -37.5000 -22.500012593.6133 11.2386 7.5000 -37.5000 -22.500011935.2334 11.2578 -7.5000 -30.0000 -22.500012783.5928 11.1608 0.0000 -30.0000 -22.500013247.3467 11.1662 7.5000 -30.0000 -22.500012540.8516 11.1905 -7.5000 -22.5000 -22.500013416.0527 11.1161 0.0000 -22.5000 -22.500013882.5576 11.1220 7.5000 -22.5000 -22.500013122.9258 11.1420 -7.5000 -15.0000 -22.500013986.9336 11.0859 0.0000 -15.0000 -22.500014475.8066 11.0888 7.5000 -15.0000 -22.500013674.1709 11.0998 -7.5000 -7.5000 -22.500014404.3320 11.0667 0.0000 -7.5000 -22.500014931.8164 11.0664 7.5000 -7.5000 -22.500014095.5020 11.0734 -7.5000 0.0000 -22.500014626.0068 11.0628 0.0000 0.0000 -22.500015178.2881 11.0624 7.5000 0.0000 -22.500014317.2451 11.0733 -7.5000 7.5000 -22.500013739.5830 11.1874 0.0000 7.5000 -22.500014239.5771 11.1897 7.5000 7.5000 -22.500013439.5391 11.2089 -7.5000 15.0000 -22.500012861.2695 11.4794 0.0000 15.0000 -22.500013340.5186 11.4846 7.5000 15.0000 -22.500012578.1133 11.5085 -7.5000 22.5000 -22.500012023.0205 11.8270 0.0000 22.5000 -22.500012468.7344 11.8310 7.5000 22.5000 -22.500011786.2598 11.8529 -7.5000 30.0000 -22.500011223.4932 12.0548 0.0000 30.0000 -22.500011652.0361 12.0578 7.5000 30.0000 -22.500011059.6875 12.0726 -7.5000 37.5000 -22.500010807.8398 12.4547 0.0000 37.5000 -22.500011288.8848 12.4552 7.5000 37.5000 -22.500010721.0156 12.4691 -7.5000 45.0000 -22.500010011.0625 12.5945 0.0000 45.0000 -22.500010491.9902 12.5978 7.5000 45.0000 -22.5000 9949.1221 12.6174 -7.5000 -45.0000 -15.000012611.6992 11.4897 0.0000 -45.0000 -15.000013055.0166 11.4958 7.5000 -45.0000 -15.000012362.9668 11.5143 -7.5000 -37.5000 -15.000012951.1133 11.5045 0.0000 -37.5000 -15.000013377.6416 11.5133 7.5000 -37.5000 -15.000012681.5947 11.5405 -7.5000 -30.0000 -15.000013635.1562 11.4264 0.0000 -30.0000 -15.000014085.9238 11.4368 7.5000 -30.0000 -15.000013331.6074 11.4671 -7.5000 -22.5000 -15.000014314.5107 11.3811 0.0000 -22.5000 -15.000014799.1006 11.3907 7.5000 -22.5000 -15.000013975.0088 11.4143 -7.5000 -15.0000 -15.000014951.4092 11.3511 0.0000 -15.0000 -15.000015483.9277 11.3580 7.5000 -15.0000 -15.000014606.8965 11.3721 -7.5000 -7.5000 -15.000015439.0049 11.3328 0.0000 -7.5000 -15.000016032.5498 11.3377 7.5000 -7.5000 -15.000015127.9463 11.3496 -7.5000 0.0000 -15.000015663.0332 11.3285 0.0000 0.0000 -15.000016257.4609 11.3344 7.5000 0.0000 -15.000015348.8447 11.3526 -7.5000 7.5000 -15.000014683.6396 11.4539 0.0000 7.5000 -15.000015200.9443 11.4625 7.5000 7.5000 -15.000014356.6992 11.4896 -7.5000 15.0000 -15.000013723.3047 11.7501 0.0000 15.0000 -15.000014239.4844 11.7595 7.5000 15.0000 -15.000013426.5576 11.7896 -7.5000 22.5000 -15.000012826.6670 12.1064 0.0000 22.5000 -15.000013308.1602 12.1132 7.5000 22.5000 -15.000012585.7520 12.1385 -7.5000 30.0000 -15.000011977.3760 12.3430 0.0000 30.0000 -15.000012451.2412 12.3491 7.5000 30.0000 -15.000011794.7617 12.3667 -7.5000 37.5000 -15.000011554.2539 12.7534 0.0000 37.5000 -15.000012054.6025 12.7584 7.5000 37.5000 -15.000011407.3086 12.7773 -7.5000 45.0000 -15.000010704.5088 12.9026 0.0000 45.0000 -15.000011217.8066 12.9109 7.5000 45.0000 -15.000010601.6152 12.9382 -7.5000 -45.0000 -7.500013295.9521 11.6056 0.0000 -45.0000 -7.500013817.1367 11.6175 7.5000 -45.0000 -7.500013129.9180 11.6376 -7.5000 -37.5000 -7.500013667.7197 11.6206 0.0000 -37.5000 -7.500014187.2695 11.6340 7.5000 -37.5000 -7.500013465.4404 11.6615 -7.5000 -30.0000 -7.500014416.3721 11.5453 0.0000 -30.0000 -7.500014950.1494 11.5589 7.5000 -30.0000 -7.500014171.1934 11.5877 -7.5000 -22.5000 -7.500015143.7334 11.5022 0.0000 -22.5000 -7.500015679.9082 11.5148 7.5000 -22.5000 -7.500014859.4189 11.5366 -7.5000 -15.0000 -7.500015873.1875 11.4715 0.0000 -15.0000 -7.500016494.9258 11.4823 7.5000 -15.0000 -7.500015600.7285 11.4959 -7.5000 -7.5000 -7.500016491.1602 11.4498 0.0000 -7.5000 -7.500017223.9004 11.4601 7.5000 -7.5000 -7.500016282.5518 11.4729 -7.5000 0.0000 -7.500016862.7988 11.4427 0.0000 0.0000 -7.500017526.7520 11.4541 7.5000 0.0000 -7.500016580.0039 11.4739 -7.5000 7.5000 -7.500015808.4473 11.5692 0.0000 7.5000 -7.500016266.6426 11.5824 7.5000 7.5000 -7.500015402.8047 11.6098 -7.5000 15.0000 -7.500014737.5664 11.8696 0.0000 15.0000 -7.500015186.9277 11.8820 7.5000 15.0000 -7.500014309.3184 11.9109 -7.5000 22.5000 -7.500013771.3047 12.2307 0.0000 22.5000 -7.500014220.7080 12.2399 7.5000 22.5000 -7.500013360.6533 12.2631 -7.5000 30.0000 -7.500012847.3564 12.4703 0.0000 30.0000 -7.500013327.6982 12.4797 7.5000 30.0000 -7.500012497.8086 12.4956 -7.5000 37.5000 -7.500012356.9111 12.8814 0.0000 37.5000 -7.500012856.6953 12.8906 7.5000 37.5000 -7.500012067.5195 12.9085 -7.5000 45.0000 -7.500011420.1025 13.0316 0.0000 45.0000 -7.500011930.2041 13.0444 7.5000 45.0000 -7.500011212.6201 13.0708 -7.5000 -45.0000 0.000013794.0518 11.6065 0.0000 -45.0000 0.000014470.9033 11.6181 7.5000 -45.0000 0.000013807.5654 11.6329 -7.5000 -37.5000 0.000014178.8291 11.6231 0.0000 -37.5000 0.000014859.4072 11.6356 7.5000 -37.5000 0.000014173.6768 11.6566 -7.5000 -30.0000 0.000014989.9434 11.5515 0.0000 -30.0000 0.000015676.7344 11.5642 7.5000 -30.0000 0.000014950.6055 11.5866 -7.5000 -22.5000 0.000015777.8623 11.5108 0.0000 -22.5000 0.000016459.9277 11.5227 7.5000 -22.5000 0.000015683.3398 11.5398 -7.5000 -15.0000 0.000016606.1270 11.4792 0.0000 -15.0000 0.000017381.4922 11.4898 7.5000 -15.0000 0.000016476.4160 11.5000 -7.5000 -7.5000 0.000017500.2305 11.4534 0.0000 -7.5000 0.000018451.3457 11.4636 7.5000 -7.5000 0.000017356.2617 11.4727 -7.5000 0.0000 0.000018190.5684 11.4434 0.0000 0.0000 0.000018922.9355 11.4547 7.5000 0.0000 0.000017763.5371 11.4692 -7.5000 7.5000 0.000017123.7109 11.5715 0.0000 7.5000 0.000017484.9551 11.5838 7.5000 7.5000 0.000016420.8203 11.6047 -7.5000 15.0000 0.000015867.6191 11.8751 0.0000 15.0000 0.000016165.0039 11.8871 7.5000 15.0000 0.000015080.9150 11.9101 -7.5000 22.5000 0.000014675.2031 12.2381 0.0000 22.5000 0.000015047.5137 12.2472 7.5000 22.5000 0.000013998.3936 12.2655 -7.5000 30.0000 0.000013547.5752 12.4769 0.0000 30.0000 0.000014000.2803 12.4862 7.5000 30.0000 0.000013043.2227 12.4983 -7.5000 37.5000 0.000012944.0605 12.8839 0.0000 37.5000 0.000013470.3574 12.8931 7.5000 37.5000 0.000012581.7432 12.9055 -7.5000 45.0000 0.000011915.0303 13.0307 0.0000 45.0000 0.000012506.3467 13.0438 7.5000 45.0000 0.000011683.8008 13.0629 -7.5000 -45.0000 7.500013269.6338 11.6058 0.0000 -45.0000 7.500013996.2744 11.6111 7.5000 -45.0000 7.500013420.9189 11.6189 -7.5000 -37.5000 7.500013633.7314 11.6248 0.0000 -37.5000 7.500014394.4863 11.6316 7.5000 -37.5000 7.500013784.3350 11.6458 -7.5000 -30.0000 7.500014463.9561 11.5536 0.0000 -30.0000 7.500015242.4619 11.5620 7.5000 -30.0000 7.500014507.6904 11.5801 -7.5000 -22.5000 7.500015274.1064 11.5125 0.0000 -22.5000 7.500016063.9229 11.5208 7.5000 -22.5000 7.500015175.1631 11.5357 -7.5000 -15.0000 7.500016107.5732 11.4803 0.0000 -15.0000 7.500016981.1387 11.4865 7.5000 -15.0000 7.500015907.3359 11.4944 -7.5000 -7.5000 7.500016898.5664 11.4537 0.0000 -7.5000 7.500017870.6738 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2714.9448 14.2469 7.5000 15.0000 45.0000 2703.1885 14.4491 -7.5000 22.5000 45.0000 2636.1086 15.0150 0.0000 22.5000 45.0000 2671.1504 14.9019 7.5000 22.5000 45.0000 2653.6355 15.0899 -7.5000 30.0000 45.0000 2567.4551 15.8305 0.0000 30.0000 45.0000 2589.7056 15.6724 7.5000 30.0000 45.0000 2576.5723 15.8389 -7.5000 37.5000 45.0000 2475.2710 16.8036 0.0000 37.5000 45.0000 2496.7502 16.6446 7.5000 37.5000 45.0000 2485.8225 16.7439 -7.5000 45.0000 45.0000 2354.6873 18.0256 0.0000 45.0000 45.0000 2373.5598 17.8854 7.5000 45.0000 45.0000 2368.8096 17.9549 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/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 $ /usr/local/freesurfer/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: /usr/local/freesurfer/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 /usr/local/freesurfer/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: /usr/local/freesurfer/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 7.5000 7.5000 0.0000 0.0000 0.0000 eta,q 0.94629 11.12401 niter,ni,del,rscale 5 3 12.0000 1.2000 parameter 6 2.889932 -> 0.500000 qaram 1.1500 parameters -1.1890 5.8356 5.8883 -1.7262 0.4653 -3.4500 eta,q 0.94814 11.09688 0.0606 0.0594 0.0583 0.0574 0.0584 0.0506 0.0580 0.0574 0.0569 0.0562 0.0569 0.0514 0.0571 0.0563 0.0562 0.0559 0.0564 0.0535 0.0582 0.0570 0.0564 0.0563 0.0559 0.0559 0.0600 0.0595 0.0574 0.0568 0.0561 0.0579 0.0600 0.0608 0.0600 0.0587 0.0564 0.0605 0.0621 0.0616 0.0644 0.0607 0.0578 0.0630 niter,ni,del,rscale 5 3 12.0000 1.2000 parameter 4 0.891894 -> 0.500000 qaram 1.1500 parameter 6 1.024662 -> 0.500000 qaram 1.3225 parameters -0.5775 6.1028 4.9156 -5.1762 2.3283 -7.4175 eta,q 0.95564 11.11213 0.0626 0.0572 0.0558 0.0516 0.0559 0.0453 0.0560 0.0528 0.0528 0.0507 0.0529 0.0442 0.0519 0.0509 0.0519 0.0508 0.0521 0.0457 0.0519 0.0522 0.0525 0.0520 0.0506 0.0490 0.0531 0.0538 0.0540 0.0537 0.0489 0.0528 0.0546 0.0542 0.0553 0.0547 0.0492 0.0568 0.0578 0.0543 0.0578 0.0551 0.0522 0.0606 niter,ni,del,rscale 6 3 12.0000 1.2000 parameters -0.5782 6.7909 4.5436 -5.8028 2.2680 -8.0261 eta,q 0.95605 11.09616 0.0577 0.0560 0.0524 0.0506 0.0520 0.0534 0.0510 0.0507 0.0472 0.0471 0.0486 0.0489 0.0458 0.0461 0.0450 0.0442 0.0456 0.0451 0.0444 0.0444 0.0446 0.0445 0.0441 0.0441 0.0463 0.0461 0.0462 0.0473 0.0454 0.0469 0.0511 0.0487 0.0495 0.0497 0.0484 0.0515 0.0575 0.0511 0.0537 0.0513 0.0526 0.0560 niter,ni,del,rscale 5 3 12.0000 1.2000 parameters -0.4750 6.8961 4.4749 -5.7893 2.2903 -8.1250 eta,q 0.95598 11.09199 0.0578 0.0545 0.0531 0.0517 0.0520 0.0545 0.0512 0.0490 0.0475 0.0482 0.0485 0.0500 0.0460 0.0447 0.0448 0.0446 0.0456 0.0457 0.0440 0.0440 0.0440 0.0440 0.0440 0.0440 0.0456 0.0465 0.0453 0.0462 0.0452 0.0460 0.0502 0.0497 0.0487 0.0487 0.0480 0.0504 0.0572 0.0524 0.0528 0.0507 0.0523 0.0549 niter,ni,del,rscale 4 3 12.0000 1.2000 parameters -0.4459 6.8930 4.4642 -5.7664 2.2983 -8.1439 eta,q 0.95597 11.09192 0.0574 0.0542 0.0534 0.0517 0.0519 0.0547 0.0510 0.0486 0.0476 0.0482 0.0484 0.0502 0.0459 0.0445 0.0448 0.0445 0.0456 0.0458 0.0440 0.0440 0.0440 0.0440 0.0440 0.0440 0.0457 0.0466 0.0453 0.0462 0.0452 0.0459 0.0503 0.0499 0.0486 0.0487 0.0480 0.0503 0.0575 0.0526 0.0527 0.0506 0.0523 0.0548 registration optimization eta report parameter search radius 6.0000 6.0000 6.0000 6.9000 6.0000 7.9350 100000*second partial in parameter space 37. 25. 25. 14. 22. 16. 0.0574 0.0542 0.0534 0.0517 0.0519 0.0547 0.0510 0.0486 0.0476 0.0482 0.0484 0.0502 0.0459 0.0445 0.0448 0.0445 0.0456 0.0458 0.0440 0.0440 0.0440 0.0440 0.0440 0.0440 0.0457 0.0466 0.0453 0.0462 0.0452 0.0459 0.0503 0.0499 0.0486 0.0487 0.0480 0.0503 0.0575 0.0526 0.0527 0.0506 0.0523 0.0548 -0.4459 6.8930 4.4642 -5.7664 2.2983 -8.1439 eta,q 0.95597 11.09192 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/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 $ /usr/local/freesurfer/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: /usr/local/freesurfer/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 /usr/local/freesurfer/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: /usr/local/freesurfer/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 -0.4459 6.8930 4.4642 -1.0881 -1.5665 -0.5861 14.4932 -2.5264 -14.1546 10.5112 4.0102 -10.0392 eta,q 0.95822 11.09406 niter,ni,del,rscale 5 3 5.0000 1.2000 parameter 4 5.179659 -> 0.500000 qaram 1.1500 parameter 5 3.318351 -> 0.500000 qaram 1.1500 parameter 9 -0.507238 -> -0.500000 qaram 1.1500 parameters -0.2303 6.6867 3.6084 -5.2281 -5.7065 -4.0158 12.2810 -0.3693 -10.0146 8.6404 5.2310 -8.6482 eta,q 0.97435 11.26471 0.0445 0.0431 0.0423 0.0314 0.0263 0.0286 0.0292 0.0363 0.0314 0.0280 0.0283 0.0282 0.0432 0.0423 0.0416 0.0336 0.0279 0.0279 0.0279 0.0327 0.0295 0.0266 0.0271 0.0271 0.0423 0.0418 0.0414 0.0372 0.0308 0.0278 0.0273 0.0295 0.0279 0.0259 0.0262 0.0262 0.0418 0.0418 0.0417 0.0414 0.0345 0.0286 0.0277 0.0273 0.0267 0.0260 0.0258 0.0257 0.0419 0.0420 0.0424 0.0457 0.0384 0.0308 0.0290 0.0267 0.0261 0.0272 0.0258 0.0257 0.0425 0.0427 0.0434 0.0498 0.0422 0.0351 0.0309 0.0276 0.0261 0.0293 0.0262 0.0260 0.0438 0.0436 0.0447 0.0536 0.0457 0.0408 0.0333 0.0299 0.0267 0.0321 0.0271 0.0269 niter,ni,del,rscale 7 3 5.0000 1.2000 parameter 5 0.513719 -> 0.500000 qaram 1.3225 parameters -0.3262 6.8300 4.0087 -9.0742 -10.4675 -0.8761 12.3160 -1.1612 -11.3322 7.9774 5.3462 -8.8796 eta,q 0.97766 11.31154 0.0297 0.0291 0.0281 0.0265 0.0245 0.0277 0.0258 0.0279 0.0245 0.0253 0.0241 0.0238 0.0274 0.0273 0.0269 0.0250 0.0234 0.0261 0.0241 0.0246 0.0231 0.0236 0.0232 0.0230 0.0260 0.0261 0.0261 0.0242 0.0232 0.0245 0.0230 0.0228 0.0224 0.0226 0.0226 0.0225 0.0256 0.0256 0.0256 0.0256 0.0244 0.0233 0.0225 0.0225 0.0224 0.0224 0.0224 0.0223 0.0263 0.0259 0.0256 0.0292 0.0272 0.0226 0.0229 0.0239 0.0231 0.0229 0.0225 0.0226 0.0279 0.0268 0.0260 0.0339 0.0310 0.0225 0.0240 0.0268 0.0244 0.0244 0.0231 0.0231 0.0303 0.0283 0.0269 0.0388 0.0351 0.0239 0.0258 0.0308 0.0262 0.0267 0.0241 0.0240 niter,ni,del,rscale 7 3 5.0000 1.2000 parameters -0.3326 7.4481 4.1004 -9.5794 -11.5276 -1.3485 12.7670 -1.2482 -11.5516 8.0596 5.5503 -9.5910 eta,q 0.97755 11.27050 0.0262 0.0263 0.0240 0.0275 0.0269 0.0255 0.0258 0.0283 0.0250 0.0255 0.0239 0.0236 0.0241 0.0244 0.0230 0.0256 0.0248 0.0240 0.0241 0.0250 0.0236 0.0239 0.0232 0.0229 0.0228 0.0231 0.0224 0.0237 0.0231 0.0229 0.0230 0.0231 0.0227 0.0228 0.0227 0.0225 0.0223 0.0223 0.0222 0.0222 0.0223 0.0225 0.0225 0.0225 0.0225 0.0225 0.0225 0.0225 0.0228 0.0222 0.0223 0.0225 0.0231 0.0224 0.0227 0.0232 0.0229 0.0228 0.0226 0.0228 0.0241 0.0226 0.0228 0.0256 0.0260 0.0239 0.0236 0.0253 0.0238 0.0238 0.0230 0.0233 0.0262 0.0236 0.0237 0.0304 0.0304 0.0274 0.0251 0.0286 0.0253 0.0254 0.0238 0.0241 niter,ni,del,rscale 6 3 5.0000 1.2000 parameters -0.3208 7.6739 4.1591 -9.4664 -11.7888 -1.3832 12.8174 -1.2846 -11.5638 8.2284 5.5542 -9.8755 eta,q 0.97759 11.26536 0.0259 0.0253 0.0241 0.0279 0.0274 0.0256 0.0254 0.0283 0.0251 0.0254 0.0238 0.0238 0.0240 0.0239 0.0232 0.0260 0.0253 0.0242 0.0238 0.0250 0.0236 0.0238 0.0231 0.0230 0.0229 0.0229 0.0227 0.0241 0.0234 0.0230 0.0228 0.0230 0.0227 0.0227 0.0226 0.0225 0.0225 0.0225 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0228 0.0226 0.0226 0.0222 0.0227 0.0223 0.0227 0.0231 0.0228 0.0227 0.0226 0.0227 0.0240 0.0232 0.0231 0.0246 0.0249 0.0234 0.0237 0.0251 0.0237 0.0236 0.0230 0.0232 0.0259 0.0244 0.0240 0.0290 0.0289 0.0265 0.0254 0.0284 0.0251 0.0251 0.0239 0.0239 niter,ni,del,rscale 5 3 5.0000 1.2000 parameters -0.3286 7.7304 4.1694 -9.4297 -11.8527 -1.3882 12.8236 -1.2850 -11.5520 8.3140 5.5366 -9.9773 eta,q 0.97759 11.26482 0.0259 0.0249 0.0240 0.0278 0.0276 0.0257 0.0254 0.0284 0.0251 0.0253 0.0238 0.0238 0.0240 0.0236 0.0232 0.0260 0.0254 0.0242 0.0238 0.0250 0.0236 0.0237 0.0230 0.0230 0.0228 0.0227 0.0226 0.0241 0.0235 0.0230 0.0228 0.0230 0.0227 0.0227 0.0226 0.0225 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0228 0.0227 0.0226 0.0222 0.0226 0.0223 0.0227 0.0230 0.0227 0.0227 0.0225 0.0227 0.0240 0.0234 0.0231 0.0247 0.0247 0.0234 0.0237 0.0251 0.0236 0.0236 0.0230 0.0231 0.0259 0.0247 0.0240 0.0291 0.0286 0.0264 0.0254 0.0283 0.0250 0.0251 0.0239 0.0239 niter,ni,del,rscale 4 3 5.0000 1.2000 parameters -0.3313 7.7466 4.1668 -9.4223 -11.8656 -1.3886 12.8260 -1.2821 -11.5417 8.3438 5.5363 -9.9983 eta,q 0.97759 11.26474 0.0259 0.0248 0.0240 0.0278 0.0276 0.0257 0.0253 0.0284 0.0251 0.0252 0.0239 0.0239 0.0240 0.0235 0.0232 0.0260 0.0255 0.0242 0.0238 0.0250 0.0236 0.0237 0.0231 0.0230 0.0228 0.0227 0.0226 0.0241 0.0236 0.0230 0.0228 0.0230 0.0227 0.0227 0.0226 0.0225 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0228 0.0227 0.0226 0.0222 0.0226 0.0223 0.0227 0.0230 0.0227 0.0227 0.0225 0.0226 0.0240 0.0235 0.0231 0.0248 0.0246 0.0234 0.0237 0.0251 0.0236 0.0237 0.0230 0.0231 0.0259 0.0248 0.0240 0.0292 0.0285 0.0264 0.0254 0.0283 0.0250 0.0251 0.0239 0.0238 registration optimization eta report parameter search radius 2.4000 2.4000 2.4000 8.2800 9.5220 7.2000 7.2000 7.2000 8.2800 7.2000 7.2000 7.2000 100000*second partial in parameter space 61. 41. 28. 9. 6. 7. 6. 11. 4. 5. 3. 3. 0.0259 0.0248 0.0240 0.0278 0.0276 0.0257 0.0253 0.0284 0.0251 0.0252 0.0239 0.0239 0.0240 0.0235 0.0232 0.0260 0.0255 0.0242 0.0238 0.0250 0.0236 0.0237 0.0231 0.0230 0.0228 0.0227 0.0226 0.0241 0.0236 0.0230 0.0228 0.0230 0.0227 0.0227 0.0226 0.0225 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0224 0.0228 0.0227 0.0226 0.0222 0.0226 0.0223 0.0227 0.0230 0.0227 0.0227 0.0225 0.0226 0.0240 0.0235 0.0231 0.0248 0.0246 0.0234 0.0237 0.0251 0.0236 0.0237 0.0230 0.0231 0.0259 0.0248 0.0240 0.0292 0.0285 0.0264 0.0254 0.0283 0.0250 0.0251 0.0239 0.0238 -0.3313 7.7466 4.1668 -9.4223 -11.8656 -1.3886 12.8260 -1.2821 -11.5417 8.3438 5.5363 -9.9983 eta,q 0.97759 11.26474 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/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 $ /usr/local/freesurfer/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: /usr/local/freesurfer/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 /usr/local/freesurfer/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: /usr/local/freesurfer/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 -0.3313 7.7466 4.1668 -9.4223 -11.8656 -1.3886 12.8260 -1.2821 -11.5417 8.3438 5.5363 -9.9983 eta,q 0.97759 11.26474 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters -0.3274 7.7377 4.2057 -8.2783 -11.1357 -1.3486 12.6142 -1.2223 -11.3685 8.3102 5.4138 -9.9669 eta,q 0.97803 11.29174 0.0240 0.0235 0.0232 0.0255 0.0240 0.0235 0.0234 0.0252 0.0231 0.0234 0.0227 0.0227 0.0231 0.0229 0.0228 0.0244 0.0232 0.0227 0.0226 0.0235 0.0225 0.0226 0.0223 0.0223 0.0226 0.0225 0.0225 0.0233 0.0225 0.0222 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0224 0.0224 0.0224 0.0224 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0226 0.0225 0.0225 0.0220 0.0220 0.0220 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0231 0.0229 0.0227 0.0225 0.0224 0.0224 0.0228 0.0234 0.0224 0.0226 0.0224 0.0223 0.0240 0.0235 0.0231 0.0239 0.0232 0.0237 0.0237 0.0251 0.0230 0.0234 0.0228 0.0227 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters -0.3442 7.6247 4.2711 -8.2820 -11.0009 -1.1469 12.5716 -1.2147 -11.3495 8.2859 5.3324 -9.8616 eta,q 0.97805 11.29807 0.0234 0.0227 0.0226 0.0242 0.0233 0.0232 0.0232 0.0245 0.0228 0.0231 0.0226 0.0226 0.0226 0.0223 0.0223 0.0232 0.0227 0.0225 0.0225 0.0231 0.0223 0.0224 0.0222 0.0222 0.0221 0.0220 0.0221 0.0224 0.0222 0.0221 0.0221 0.0222 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0220 0.0219 0.0220 0.0221 0.0221 0.0220 0.0221 0.0220 0.0220 0.0221 0.0222 0.0220 0.0221 0.0220 0.0220 0.0226 0.0225 0.0222 0.0230 0.0224 0.0222 0.0225 0.0231 0.0223 0.0224 0.0222 0.0222 0.0234 0.0230 0.0225 0.0245 0.0233 0.0231 0.0232 0.0244 0.0228 0.0231 0.0226 0.0225 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters -0.3480 7.5910 4.2412 -8.2181 -10.9299 -1.0649 12.5617 -1.2066 -11.3351 8.2954 5.3230 -9.8714 eta,q 0.97806 11.30180 0.0230 0.0226 0.0224 0.0237 0.0229 0.0228 0.0229 0.0238 0.0226 0.0228 0.0224 0.0224 0.0224 0.0222 0.0222 0.0230 0.0224 0.0223 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0220 0.0220 0.0223 0.0221 0.0220 0.0221 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0222 0.0220 0.0220 0.0220 0.0220 0.0224 0.0223 0.0222 0.0227 0.0223 0.0222 0.0223 0.0228 0.0222 0.0223 0.0221 0.0222 0.0230 0.0227 0.0224 0.0238 0.0229 0.0228 0.0229 0.0238 0.0226 0.0228 0.0224 0.0224 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters -0.3467 7.5719 4.2351 -8.1430 -10.8779 -1.0028 12.5514 -1.2066 -11.3326 8.3148 5.3063 -9.8899 eta,q 0.97807 11.30457 0.0227 0.0224 0.0223 0.0233 0.0226 0.0225 0.0226 0.0233 0.0224 0.0225 0.0223 0.0222 0.0223 0.0221 0.0221 0.0227 0.0223 0.0222 0.0222 0.0225 0.0221 0.0222 0.0221 0.0221 0.0220 0.0220 0.0220 0.0222 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0223 0.0222 0.0221 0.0225 0.0222 0.0221 0.0222 0.0225 0.0221 0.0222 0.0221 0.0221 0.0227 0.0224 0.0223 0.0233 0.0226 0.0225 0.0226 0.0233 0.0224 0.0225 0.0223 0.0222 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters -0.3499 7.5612 4.2323 -8.0787 -10.8375 -0.9650 12.5544 -1.2027 -11.3172 8.3467 5.2883 -9.9279 eta,q 0.97807 11.30657 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0223 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0220 0.0224 0.0221 0.0221 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0220 0.0220 0.0220 0.0220 0.0219 0.0220 0.0222 0.0221 0.0220 0.0223 0.0221 0.0220 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 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 77. 49. 33. 16. 8. 5. 7. 15. 5. 6. 4. 4. 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0223 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0220 0.0224 0.0221 0.0221 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0220 0.0220 0.0220 0.0220 0.0219 0.0220 0.0222 0.0221 0.0220 0.0223 0.0221 0.0220 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 -0.3499 7.5612 4.2323 -8.0787 -10.8375 -0.9650 12.5544 -1.2027 -11.3172 8.3467 5.2883 -9.9279 eta,q 0.97807 11.30657 --------------------------------------------------------------------- imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/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 $ /usr/local/freesurfer/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: /usr/local/freesurfer/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 /usr/local/freesurfer/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: /usr/local/freesurfer/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 -0.3499 7.5612 4.2323 -8.0787 -10.8375 -0.9650 12.5544 -1.2027 -11.3172 8.3467 5.2883 -9.9279 eta,q 0.97807 11.30657 niter,ni,del,rscale 5 3 5.0000 0.8000 parameters -0.3521 7.5557 4.2152 -8.4955 -11.0219 -1.1991 12.5980 -1.1868 -11.3674 8.2879 5.3447 -9.8063 eta,q 0.97801 11.29655 0.0239 0.0231 0.0227 0.0244 0.0235 0.0234 0.0236 0.0252 0.0230 0.0234 0.0228 0.0228 0.0228 0.0225 0.0223 0.0233 0.0228 0.0226 0.0227 0.0234 0.0224 0.0226 0.0223 0.0223 0.0221 0.0221 0.0220 0.0224 0.0222 0.0222 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0221 0.0220 0.0223 0.0221 0.0220 0.0221 0.0223 0.0221 0.0222 0.0221 0.0221 0.0228 0.0225 0.0223 0.0237 0.0228 0.0225 0.0227 0.0234 0.0225 0.0226 0.0223 0.0223 0.0239 0.0232 0.0228 0.0259 0.0240 0.0240 0.0235 0.0251 0.0231 0.0235 0.0228 0.0227 niter,ni,del,rscale 4 3 5.0000 0.7000 parameters -0.3394 7.5925 4.2224 -8.3416 -10.9619 -1.1412 12.5848 -1.1989 -11.3560 8.2693 5.3337 -9.8382 eta,q 0.97805 11.29904 0.0234 0.0229 0.0226 0.0243 0.0233 0.0231 0.0232 0.0245 0.0228 0.0231 0.0226 0.0225 0.0226 0.0224 0.0223 0.0234 0.0226 0.0225 0.0225 0.0231 0.0223 0.0224 0.0222 0.0222 0.0222 0.0221 0.0221 0.0225 0.0222 0.0221 0.0221 0.0222 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0221 0.0221 0.0220 0.0220 0.0220 0.0221 0.0222 0.0221 0.0221 0.0220 0.0220 0.0226 0.0224 0.0223 0.0228 0.0225 0.0223 0.0225 0.0231 0.0223 0.0225 0.0222 0.0222 0.0234 0.0229 0.0226 0.0243 0.0233 0.0232 0.0232 0.0245 0.0228 0.0231 0.0226 0.0225 niter,ni,del,rscale 3 3 5.0000 0.6000 parameters -0.3425 7.5826 4.2352 -8.2283 -10.9235 -1.0680 12.5693 -1.2015 -11.3407 8.2913 5.3224 -9.8702 eta,q 0.97806 11.30193 0.0230 0.0226 0.0224 0.0238 0.0229 0.0228 0.0229 0.0238 0.0226 0.0228 0.0224 0.0224 0.0224 0.0223 0.0222 0.0230 0.0224 0.0223 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0220 0.0220 0.0223 0.0221 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0222 0.0220 0.0220 0.0220 0.0220 0.0224 0.0223 0.0222 0.0226 0.0223 0.0222 0.0224 0.0228 0.0222 0.0223 0.0221 0.0222 0.0230 0.0226 0.0224 0.0238 0.0230 0.0228 0.0229 0.0238 0.0226 0.0228 0.0224 0.0224 niter,ni,del,rscale 2 3 5.0000 0.5000 parameters -0.3470 7.5720 4.2373 -8.1423 -10.8767 -1.0056 12.5595 -1.2058 -11.3377 8.3130 5.3073 -9.8880 eta,q 0.97807 11.30453 0.0227 0.0224 0.0223 0.0233 0.0226 0.0225 0.0226 0.0233 0.0224 0.0225 0.0223 0.0222 0.0223 0.0221 0.0221 0.0227 0.0223 0.0222 0.0222 0.0225 0.0221 0.0222 0.0221 0.0221 0.0220 0.0220 0.0220 0.0222 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0223 0.0222 0.0221 0.0224 0.0222 0.0221 0.0222 0.0225 0.0221 0.0222 0.0221 0.0221 0.0227 0.0224 0.0223 0.0233 0.0226 0.0224 0.0226 0.0233 0.0224 0.0225 0.0223 0.0222 niter,ni,del,rscale 1 3 5.0000 0.4000 parameters -0.3509 7.5618 4.2329 -8.0822 -10.8342 -0.9610 12.5495 -1.2052 -11.3228 8.3499 5.2833 -9.9133 eta,q 0.97807 11.30664 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0223 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0220 0.0224 0.0221 0.0221 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0222 0.0221 0.0220 0.0223 0.0221 0.0220 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 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 77. 48. 33. 16. 8. 5. 7. 15. 5. 6. 4. 4. 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0223 0.0228 0.0222 0.0223 0.0221 0.0221 0.0221 0.0221 0.0220 0.0224 0.0221 0.0221 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0221 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0219 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0220 0.0222 0.0221 0.0220 0.0223 0.0221 0.0220 0.0221 0.0223 0.0221 0.0221 0.0220 0.0220 0.0224 0.0222 0.0221 0.0228 0.0224 0.0222 0.0224 0.0228 0.0222 0.0223 0.0221 0.0221 -0.3509 7.5618 4.2329 -8.0822 -10.8342 -0.9610 12.5495 -1.2052 -11.3228 8.3499 5.2833 -9.9133 eta,q 0.97807 11.30664 --------------------------------------------------------------------- compute_vox2vox talsrcimg talsrcimg_to_711-2C_as_mni_average_305_t4 /usr/local/freesurfer/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: /usr/local/freesurfer/average/711-2C_as_mni_average_305.4dfp.ifh Writing: talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt start time Fri Jun 19 13:19:27 CEST 2009 end time Fri Jun 19 13:20:35 CEST 2009 mpr2mni305 success -------------------------------------------- tkregister2_cmdl --mov nu.mgz --targ /usr/local/freesurfer/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 0.919 0.125 0.012 -6.898; -0.113 0.892 -0.083 31.403; -0.053 0.099 0.990 -0.473; 0.000 0.000 0.000 1.000; target volume /usr/local/freesurfer/average/mni305.cor.mgz movable volume nu.mgz reg file talsrcimg.reg.tmp.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 INFO: loading target /usr/local/freesurfer/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; 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) -------- 0.919 -0.012 0.125 -0.363; 0.053 0.990 -0.099 4.223; -0.113 0.083 0.892 7.645; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.919 -0.012 0.125 -0.363; 0.053 0.990 -0.099 4.223; -0.113 0.083 0.892 7.645; 0.000 0.000 0.000 1.000; subject = subject-unknown RegMat --------------------------- 0.919 -0.012 0.125 -0.363; 0.053 0.990 -0.099 4.223; -0.113 0.083 0.892 7.645; 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' -------------------------------------------- Fri Jun 19 13:20:36 CEST 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Jun 19 13:20:37 CEST 2009 /data/MOODS2/freesurfer/1005/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6931, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /data/MOODS2/freesurfer/1005/mri/transforms/talairach_avi.log TalAviQA: 0.97807 z-score: 0 #-------------------------------------------- #@# Intensity Normalization Fri Jun 19 13:20:38 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.068 0.025 -0.148 -0.214; -0.043 0.999 0.117 -20.701; 0.140 -0.090 1.092 1.256; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 2 minutes and 6 seconds. white matter peak found at 111 gm peak at 88 (88), valley at 50 (50) csf peak at 45, setting threshold to 73 white matter peak found at 111 gm peak at 86 (86), valley at 49 (49) csf peak at 43, setting threshold to 71 #-------------------------------------------- #@# Skull Stripping Fri Jun 19 13:22:45 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 using (100, 105, 115) as brain centroid... mean wm in atlas = 126, using box (80,77,89) --> (120, 132,140) to find MRI wm before smoothing, mri peak at 100 after smoothing, mri peak at 99, scaling input intensities by 1.273 scaling channel 0 by 1.27273 initial log_p = -17522.8 ************************************************ First Search limited to translation only. ************************************************ using real data threshold=12.0 Found translation: (-1.7, 2.8, -11.9): log p = -18664.5 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16541.3, old_max_log_p =-18664.5 (thresh=-18645.9) 1.041 -0.119 -0.117 20.978; 0.154 1.172 0.175 -57.805; 0.098 -0.167 1.037 -1.404; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16520.6, old_max_log_p =-16541.3 (thresh=-16524.8) 1.110 -0.149 0.020 0.481; 0.164 1.246 0.186 -68.988; -0.037 -0.141 0.978 18.995; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16503.0, old_max_log_p =-16520.6 (thresh=-16504.1) 1.106 -0.129 -0.108 12.914; 0.153 1.168 0.174 -57.107; 0.109 -0.159 0.972 3.387; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16503.0, old_max_log_p =-16503.0 (thresh=-16486.5) 1.106 -0.129 -0.108 12.914; 0.153 1.168 0.174 -57.107; 0.109 -0.159 0.972 3.387; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16421.8, old_max_log_p =-16503.0 (thresh=-16486.5) 1.140 -0.133 -0.111 9.388; 0.153 1.168 0.174 -57.107; 0.110 -0.162 0.987 1.833; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16421.8, old_max_log_p =-16421.8 (thresh=-16405.3) 1.140 -0.133 -0.111 9.388; 0.153 1.168 0.174 -57.107; 0.110 -0.162 0.987 1.833; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-16413.8, old_max_log_p =-16421.8 (thresh=-16405.3) 1.136 -0.133 -0.111 9.842; 0.153 1.163 0.174 -56.410; 0.110 -0.162 0.987 1.833; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.13588 -0.13271 -0.11060 9.84237; 0.15280 1.16324 0.17351 -56.41043; 0.11024 -0.16170 0.98695 1.83343; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.13588 -0.13271 -0.11060 9.84237; 0.15280 1.16324 0.17351 -56.41043; 0.11024 -0.16170 0.98695 1.83343; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 007: -log(p) = 16413.8 tol 0.000010 Resulting transform: 1.136 -0.133 -0.111 9.842; 0.153 1.163 0.174 -56.410; 0.110 -0.162 0.987 1.833; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -16413.8 (old=-17522.8) transform before final EM align: 1.136 -0.133 -0.111 9.842; 0.153 1.163 0.174 -56.410; 0.110 -0.162 0.987 1.833; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.13588 -0.13271 -0.11060 9.84237; 0.15280 1.16324 0.17351 -56.41043; 0.11024 -0.16170 0.98695 1.83343; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.13588 -0.13271 -0.11060 9.84237; 0.15280 1.16324 0.17351 -56.41043; 0.11024 -0.16170 0.98695 1.83343; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 006: -log(p) = 2137360.5 after pass:transform: ( 1.13, -0.13, -0.10, 9.84) ( 0.17, 1.18, 0.19, -56.41) ( 0.11, -0.16, 0.99, 1.83) dfp_em_step_func: 007: -log(p) = 2108904.0 after pass:transform: ( 1.13, -0.13, -0.11, 9.84) ( 0.16, 1.17, 0.18, -56.41) ( 0.11, -0.16, 0.99, 1.83) dfp_em_step_func: 008: -log(p) = 2104285.2 after pass:transform: ( 1.13, -0.13, -0.11, 9.84) ( 0.16, 1.17, 0.18, -56.41) ( 0.11, -0.16, 0.99, 1.83) dfp_em_step_func: 009: -log(p) = 2100892.5 after pass:transform: ( 1.12, -0.14, -0.10, 9.84) ( 0.17, 1.17, 0.18, -56.41) ( 0.12, -0.15, 0.99, 1.83) dfp_em_step_func: 010: -log(p) = 2099461.0 after pass:transform: ( 1.12, -0.14, -0.10, 9.84) ( 0.17, 1.17, 0.18, -56.41) ( 0.12, -0.15, 0.99, 1.83) dfp_em_step_func: 011: -log(p) = 2089880.5 after pass:transform: ( 1.11, -0.14, -0.09, 9.84) ( 0.18, 1.17, 0.18, -56.41) ( 0.11, -0.14, 0.99, 1.83) dfp_em_step_func: 012: -log(p) = 2088910.0 after pass:transform: ( 1.10, -0.14, -0.08, 9.84) ( 0.18, 1.17, 0.18, -56.41) ( 0.11, -0.14, 0.98, 1.83) dfp_em_step_func: 013: -log(p) = 2057900.4 after pass:transform: ( 1.08, -0.14, -0.05, 9.84) ( 0.19, 1.15, 0.17, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 014: -log(p) = 2049778.9 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.96, 1.83) dfp_em_step_func: 015: -log(p) = 2047160.5 after pass:transform: ( 1.06, -0.14, -0.03, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.96, 1.83) dfp_em_step_func: 016: -log(p) = 2041165.5 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 017: -log(p) = 2039868.5 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 018: -log(p) = 2038672.8 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 019: -log(p) = 2037140.4 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.19, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 020: -log(p) = 2036968.9 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.20, 1.15, 0.16, -56.41) ( 0.10, -0.13, 0.97, 1.83) dfp_em_step_func: 021: -log(p) = 2035224.2 after pass:transform: ( 1.07, -0.13, -0.04, 9.84) ( 0.20, 1.15, 0.16, -56.41) ( 0.09, -0.12, 0.97, 1.83) dfp_em_step_func: 022: -log(p) = 2034942.0 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.21, 1.16, 0.14, -56.41) ( 0.09, -0.12, 0.97, 1.83) dfp_em_step_func: 023: -log(p) = 2032550.2 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.21, 1.16, 0.14, -56.41) ( 0.08, -0.12, 0.98, 1.83) dfp_em_step_func: 024: -log(p) = 2030973.4 after pass:transform: ( 1.06, -0.13, -0.04, 9.84) ( 0.20, 1.16, 0.14, -56.41) ( 0.08, -0.12, 0.98, 1.83) dfp_em_step_func: 025: -log(p) = 2030751.9 after pass:transform: ( 1.06, -0.13, -0.04, 9.84) ( 0.21, 1.16, 0.14, -56.41) ( 0.08, -0.12, 0.98, 1.83) dfp_em_step_func: 026: -log(p) = 2030394.5 after pass:transform: ( 1.06, -0.13, -0.04, 9.84) ( 0.21, 1.16, 0.14, -56.41) ( 0.08, -0.12, 0.98, 1.83) dfp_em_step_func: 027: -log(p) = 2029895.8 after pass:transform: ( 1.06, -0.13, -0.04, 9.84) ( 0.21, 1.16, 0.14, -56.41) ( 0.08, -0.11, 0.98, 1.83) dfp_em_step_func: 028: -log(p) = 2029351.8 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.21, 1.16, 0.13, -56.41) ( 0.07, -0.11, 0.98, 1.83) dfp_em_step_func: 029: -log(p) = 2029289.8 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.21, 1.16, 0.13, -56.41) ( 0.07, -0.11, 0.98, 1.83) dfp_em_step_func: 030: -log(p) = 2028325.9 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.21, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 031: -log(p) = 2026328.0 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.06, -0.10, 0.98, 1.83) dfp_em_step_func: 032: -log(p) = 2026272.9 after pass:transform: ( 1.06, -0.14, -0.03, 9.84) ( 0.20, 1.17, 0.14, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 033: -log(p) = 2026054.4 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 034: -log(p) = 2026053.5 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 035: -log(p) = 2026016.6 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 036: -log(p) = 2025956.0 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) dfp_em_step_func: 037: -log(p) = 2025926.6 after pass:transform: ( 1.06, -0.13, -0.03, 9.84) ( 0.20, 1.17, 0.13, -56.41) ( 0.07, -0.10, 0.98, 1.83) 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: 039: -log(p) = 2025926.6 tol 0.000000 final transform: 1.063 -0.135 -0.031 9.842; 0.201 1.171 0.133 -56.410; 0.066 -0.101 0.976 1.833; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 18 minutes and 8 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz 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=127 y=113 z=114 r=81 first estimation of the main basin volume: 2273734 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=144, y=93, z=76, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done Analyze main basin size=10831186154 voxels, voxel volume =1.000 = 10831186154 mmm3 = 10831185.920 cm3 done PostAnalyze...Basin Prior 2 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=117, z=108, r=10357 iterations GLOBAL CSF_MIN=0, CSF_intensity=15, CSF_MAX=84 , nb = 20673 RIGHT_CER CSF_MIN=0, CSF_intensity=16, CSF_MAX=71 , nb = 1449 LEFT_CER CSF_MIN=0, CSF_intensity=14, CSF_MAX=56 , nb = 1413 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=15, CSF_MAX=90 , nb = 9000 LEFT_BRAIN CSF_MIN=0, CSF_intensity=12, CSF_MAX=83 , nb = 8550 OTHER CSF_MIN=0, CSF_intensity=25, CSF_MAX=59 , nb = 261 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 : 84, 68, 64, 84 after analyzing : 54, 68, 68, 72 RIGHT_CER before analyzing : 71, 73, 75, 96 after analyzing : 71, 74, 75, 79 LEFT_CER before analyzing : 56, 71, 78, 97 after analyzing : 56, 75, 78, 80 RIGHT_BRAIN before analyzing : 90, 71, 67, 83 after analyzing : 56, 71, 71, 74 LEFT_BRAIN before analyzing : 83, 66, 55, 105 after analyzing : 52, 66, 66, 75 OTHER before analyzing : 59, 19, 0, 15 after analyzing : 19, 24, 27, 24 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...66 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 70.335, std = 7.583 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.27, sigma = 6.38 after rotation: sse = 3.27, sigma = 6.38 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.58, its var is 7.55 before Erosion-Dilatation 1.43% of inacurate vertices after Erosion-Dilatation 2.26% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...50 iterations mri_strip_skull: done peeling brain Brain Size = 1739432 voxels, voxel volume = 1.000 mm3 = 1739432 mmm3 = 1739.432 cm3 ****************************** Save...done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Jun 19 13:42:23 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=32.1 using (103, 93, 116) as brain centroid... mean wm in atlas = 107, using box (87,78,95) --> (119, 108,137) to find MRI wm before smoothing, mri peak at 98 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 initial log_p = -23908.9 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, 5.1, -5.1): log p = -15555.4 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-12222.1, old_max_log_p =-15555.4 (thresh=-15539.8) 1.053 -0.155 -0.018 12.223; 0.131 1.106 0.129 -37.843; 0.000 -0.138 0.929 18.334; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-12164.8, old_max_log_p =-12222.1 (thresh=-12209.8) 1.053 -0.155 -0.018 12.223; 0.121 1.045 0.007 -16.147; 0.018 0.008 0.997 -8.045; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-11948.7, old_max_log_p =-12164.8 (thresh=-12152.6) 1.053 -0.155 -0.018 12.223; 0.123 1.037 0.137 -29.790; 0.002 -0.128 0.988 10.547; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-11948.7, old_max_log_p =-11948.7 (thresh=-11936.8) 1.053 -0.155 -0.018 12.223; 0.123 1.037 0.137 -29.790; 0.002 -0.128 0.988 10.547; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10989.1, old_max_log_p =-11948.7 (thresh=-11936.8) 1.037 -0.152 -0.018 14.014; 0.128 1.086 0.143 -38.705; 0.002 -0.126 0.972 13.949; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10971.3, old_max_log_p =-10989.1 (thresh=-10978.1) 1.037 -0.152 -0.018 14.014; 0.130 1.103 0.145 -41.167; 0.002 -0.126 0.972 13.949; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10971.3, old_max_log_p =-10971.3 (thresh=-10960.4) 1.037 -0.152 -0.018 14.014; 0.130 1.103 0.145 -41.167; 0.002 -0.126 0.972 13.949; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10808.2, old_max_log_p =-10971.3 (thresh=-10960.4) 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10808.2, old_max_log_p =-10808.2 (thresh=-10797.4) 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2185 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04100 -0.15286 -0.01789 13.57295; 0.13097 1.10723 0.14591 -41.79253; 0.00205 -0.12455 0.96041 15.48259; 0.00000 0.00000 0.00000 1.00000; nsamples 2185 Quasinewton: input matrix 1.04100 -0.15286 -0.01789 13.57295; 0.13097 1.10723 0.14591 -41.79253; 0.00205 -0.12455 0.96041 15.48259; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 009: -log(p) = 10808.2 tol 0.000010 Resulting transform: 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10808.2 (old=-23908.9) transform before final EM align: 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 244171 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04100 -0.15286 -0.01789 13.57295; 0.13097 1.10723 0.14591 -41.79253; 0.00205 -0.12455 0.96041 15.48259; 0.00000 0.00000 0.00000 1.00000; nsamples 244171 Quasinewton: input matrix 1.04100 -0.15286 -0.01789 13.57295; 0.13097 1.10723 0.14591 -41.79253; 0.00205 -0.12455 0.96041 15.48259; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 009: -log(p) = 1515693.6 tol 0.000000 final transform: 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 11 minutes and 41 seconds. #-------------------------------------- #@# CA Normalize Fri Jun 19 13:54:04 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=32.1 using (103, 93, 116) as brain centroid... mean wm in atlas = 107, using box (87,78,95) --> (119, 108,137) to find MRI wm before smoothing, mri peak at 98 after smoothing, mri peak at 99, scaling input intensities by 1.081 scaling channel 0 by 1.08081 using 244171 sample points... INFO: compute sample coordinates transform 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.793; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 55, 28) --> (192, 154, 200) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 112.0 1156 of 3937 (29.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 60, 28) --> (129, 163, 200) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 110.0 1486 of 4310 (34.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 133, 54) --> (181, 171, 109) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 101.0 57 of 179 (31.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 133, 52) --> (132, 176, 111) Right_Cerebellum_White_Matter: limiting intensities to 90.0 --> 101.0 21 of 119 (17.6%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 125, 90) --> (148, 188, 122) Brain_Stem: limiting intensities to 84.0 --> 98.0 40 of 319 (12.5%) samples deleted using 8864 total control points for intensity normalization... bias field = 1.011 +- 0.053 11 of 6104 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 55, 28) --> (192, 154, 200) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 108.0 1520 of 4469 (34.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 60, 28) --> (129, 163, 200) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 108.0 1733 of 4579 (37.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 133, 54) --> (181, 171, 109) Left_Cerebellum_White_Matter: limiting intensities to 85.0 --> 96.0 45 of 153 (29.4%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 133, 52) --> (132, 176, 111) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 94.0 31 of 111 (27.9%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 125, 90) --> (148, 188, 122) Brain_Stem: limiting intensities to 80.0 --> 93.0 74 of 342 (21.6%) samples deleted using 9654 total control points for intensity normalization... bias field = 1.028 +- 0.041 11 of 6251 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (123, 55, 28) --> (192, 154, 200) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 107.0 2001 of 4412 (45.4%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 60, 28) --> (129, 163, 200) Right_Cerebral_White_Matter: limiting intensities to 94.0 --> 108.0 1822 of 4495 (40.5%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 133, 54) --> (181, 171, 109) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 94.0 74 of 175 (42.3%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (90, 133, 52) --> (132, 176, 111) Right_Cerebellum_White_Matter: limiting intensities to 83.0 --> 93.0 20 of 139 (14.4%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (115, 125, 90) --> (148, 188, 122) Brain_Stem: limiting intensities to 77.0 --> 93.0 56 of 342 (16.4%) samples deleted using 9563 total control points for intensity normalization... bias field = 1.022 +- 0.032 14 of 5590 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Fri Jun 19 13:55:47 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB_all_2008-03-26.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 '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.15 (predicted orig area = 7.0) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.04 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.789, neg=0, invalid=766 0001: dt=171.980676, rms=0.745 (5.563%), neg=0, invalid=766 0002: dt=233.244444, rms=0.727 (2.353%), neg=0, invalid=766 0003: dt=169.531915, rms=0.722 (0.705%), neg=0, invalid=766 0004: dt=129.472000, rms=0.720 (0.331%), neg=0, invalid=766 0005: dt=517.888000, rms=0.715 (0.663%), neg=0, invalid=766 0006: dt=129.472000, rms=0.714 (0.154%), neg=0, invalid=766 0007: dt=129.472000, rms=0.713 (0.162%), neg=0, invalid=766 0008: dt=129.472000, rms=0.711 (0.241%), neg=0, invalid=766 0009: dt=129.472000, rms=0.709 (0.288%), neg=0, invalid=766 0010: dt=129.472000, rms=0.707 (0.321%), neg=0, invalid=766 0011: dt=129.472000, rms=0.704 (0.325%), neg=0, invalid=766 0012: dt=129.472000, rms=0.702 (0.341%), neg=0, invalid=766 0013: dt=129.472000, rms=0.700 (0.304%), neg=0, invalid=766 0014: dt=129.472000, rms=0.698 (0.273%), neg=0, invalid=766 0015: dt=129.472000, rms=0.696 (0.220%), neg=0, invalid=766 0016: dt=129.472000, rms=0.695 (0.197%), neg=0, invalid=766 0017: dt=129.472000, rms=0.693 (0.212%), neg=0, invalid=766 0018: dt=129.472000, rms=0.692 (0.210%), neg=0, invalid=766 0019: dt=129.472000, rms=0.691 (0.197%), neg=0, invalid=766 0020: dt=129.472000, rms=0.689 (0.173%), neg=0, invalid=766 0021: dt=129.472000, rms=0.689 (0.101%), neg=0, invalid=766 0022: dt=129.472000, rms=0.688 (0.116%), neg=0, invalid=766 0023: dt=129.472000, rms=0.687 (0.151%), neg=0, invalid=766 0024: dt=129.472000, rms=0.686 (0.145%), neg=0, invalid=766 0025: dt=129.472000, rms=0.685 (0.109%), neg=0, invalid=766 0026: dt=129.472000, rms=0.684 (0.112%), neg=0, invalid=766 0027: dt=129.472000, rms=0.684 (0.101%), neg=0, invalid=766 0028: dt=517.888000, rms=0.682 (0.248%), neg=0, invalid=766 0029: dt=73.984000, rms=0.682 (0.067%), neg=0, invalid=766 0030: dt=73.984000, rms=0.681 (0.005%), neg=0, invalid=766 0031: dt=73.984000, rms=0.681 (0.016%), neg=0, invalid=766 0032: dt=73.984000, rms=0.681 (0.062%), neg=0, invalid=766 0033: dt=73.984000, rms=0.680 (0.099%), neg=0, invalid=766 0034: dt=73.984000, rms=0.680 (0.093%), neg=0, invalid=766 0035: dt=73.984000, rms=0.679 (0.060%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.679, neg=0, invalid=766 0036: dt=177.454545, rms=0.675 (0.575%), neg=0, invalid=766 0037: dt=32.368000, rms=0.675 (0.041%), neg=0, invalid=766 0038: dt=32.368000, rms=0.675 (0.008%), neg=0, invalid=766 0039: dt=32.368000, rms=0.675 (-0.006%), neg=0, invalid=766 setting smoothness coefficient to 0.15 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.687, neg=0, invalid=766 0040: dt=59.178082, rms=0.684 (0.551%), neg=0, invalid=766 0041: dt=142.674033, rms=0.670 (2.034%), neg=0, invalid=766 0042: dt=19.723785, rms=0.665 (0.666%), neg=0, invalid=766 0043: dt=25.920000, rms=0.665 (0.099%), neg=0, invalid=766 0044: dt=25.920000, rms=0.663 (0.198%), neg=0, invalid=766 0045: dt=25.920000, rms=0.661 (0.375%), neg=0, invalid=766 0046: dt=25.920000, rms=0.657 (0.541%), neg=0, invalid=766 0047: dt=25.920000, rms=0.653 (0.679%), neg=0, invalid=766 0048: dt=25.920000, rms=0.648 (0.743%), neg=0, invalid=766 0049: dt=25.920000, rms=0.643 (0.709%), neg=0, invalid=766 0050: dt=25.920000, rms=0.639 (0.635%), neg=0, invalid=766 0051: dt=25.920000, rms=0.636 (0.542%), neg=0, invalid=766 0052: dt=25.920000, rms=0.633 (0.479%), neg=0, invalid=766 0053: dt=25.920000, rms=0.632 (0.073%), neg=0, invalid=766 0054: dt=25.920000, rms=0.632 (0.108%), neg=0, invalid=766 0055: dt=25.920000, rms=0.631 (0.097%), neg=0, invalid=766 0056: dt=331.776000, rms=0.630 (0.190%), neg=0, invalid=766 0057: dt=52.779221, rms=0.626 (0.521%), neg=0, invalid=766 0058: dt=3.888000, rms=0.626 (0.005%), neg=0, invalid=766 0059: dt=3.888000, rms=0.626 (0.000%), neg=0, invalid=766 0060: dt=3.888000, rms=0.626 (-0.010%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.626, neg=0, invalid=766 0061: dt=78.474114, rms=0.624 (0.376%), neg=0, invalid=766 0062: dt=38.736842, rms=0.624 (0.089%), neg=0, invalid=766 0063: dt=38.736842, rms=0.623 (0.080%), neg=0, invalid=766 0064: dt=38.736842, rms=0.622 (0.094%), neg=0, invalid=766 0065: dt=38.736842, rms=0.622 (0.110%), neg=0, invalid=766 0066: dt=38.736842, rms=0.621 (0.114%), neg=0, invalid=766 0067: dt=38.736842, rms=0.620 (0.142%), neg=0, invalid=766 0068: dt=38.736842, rms=0.620 (0.100%), neg=0, invalid=766 0069: dt=38.736842, rms=0.619 (0.098%), neg=0, invalid=766 0070: dt=331.776000, rms=0.617 (0.294%), neg=0, invalid=766 0071: dt=15.552000, rms=0.617 (0.018%), neg=0, invalid=766 0072: dt=15.552000, rms=0.617 (0.012%), neg=0, invalid=766 0073: dt=15.552000, rms=0.617 (-0.003%), neg=0, invalid=766 setting smoothness coefficient to 0.59 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.647, neg=0, invalid=766 0074: dt=19.303644, rms=0.644 (0.494%), neg=0, invalid=766 0075: dt=60.745763, rms=0.638 (0.984%), neg=0, invalid=766 0076: dt=27.169811, rms=0.635 (0.473%), neg=0, invalid=766 0077: dt=23.176080, rms=0.632 (0.445%), neg=0, invalid=766 0078: dt=16.000000, rms=0.631 (0.192%), neg=0, invalid=766 0079: dt=16.000000, rms=0.630 (0.165%), neg=0, invalid=766 0080: dt=16.000000, rms=0.628 (0.221%), neg=0, invalid=766 0081: dt=16.000000, rms=0.627 (0.268%), neg=0, invalid=766 0082: dt=16.000000, rms=0.625 (0.274%), neg=0, invalid=766 0083: dt=16.000000, rms=0.623 (0.282%), neg=0, invalid=766 0084: dt=16.000000, rms=0.622 (0.233%), neg=0, invalid=766 0085: dt=16.000000, rms=0.620 (0.193%), neg=0, invalid=766 0086: dt=16.000000, rms=0.619 (0.172%), neg=0, invalid=766 0087: dt=16.000000, rms=0.619 (0.145%), neg=0, invalid=766 0088: dt=16.000000, rms=0.618 (0.101%), neg=0, invalid=766 0089: dt=16.000000, rms=0.617 (0.064%), neg=0, invalid=766 0090: dt=25.600000, rms=0.617 (0.028%), neg=0, invalid=766 0091: dt=25.600000, rms=0.617 (-0.073%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.617, neg=0, invalid=766 0092: dt=0.000000, rms=0.617 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.673, neg=0, invalid=766 0093: dt=0.252000, rms=0.673 (0.011%), neg=0, invalid=766 0094: dt=0.063000, rms=0.673 (0.003%), neg=0, invalid=766 0095: dt=0.063000, rms=0.673 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=766 0096: dt=0.432000, rms=0.673 (0.021%), neg=0, invalid=766 0097: dt=0.144000, rms=0.673 (0.003%), neg=0, invalid=766 0098: dt=0.144000, rms=0.673 (0.000%), neg=0, invalid=766 0099: dt=0.144000, rms=0.673 (-0.011%), neg=0, invalid=766 setting smoothness coefficient to 5.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.764, neg=0, invalid=766 0100: dt=0.892093, rms=0.744 (2.654%), neg=0, invalid=766 0101: dt=1.541463, rms=0.736 (1.010%), neg=0, invalid=766 0102: dt=2.391304, rms=0.731 (0.710%), neg=0, invalid=766 0103: dt=1.222727, rms=0.729 (0.356%), neg=0, invalid=766 0104: dt=0.841060, rms=0.728 (0.112%), neg=0, invalid=766 0105: dt=0.841060, rms=0.727 (0.121%), neg=0, invalid=766 0106: dt=0.841060, rms=0.726 (0.152%), neg=0, invalid=766 0107: dt=0.841060, rms=0.725 (0.120%), neg=0, invalid=766 0108: dt=0.841060, rms=0.725 (0.026%), neg=0, invalid=766 0109: dt=1.280000, rms=0.724 (0.041%), neg=0, invalid=766 0110: dt=1.024000, rms=0.724 (0.035%), neg=0, invalid=766 0111: dt=1.024000, rms=0.724 (0.023%), neg=0, invalid=766 0112: dt=1.024000, rms=0.724 (0.034%), neg=0, invalid=766 0113: dt=1.024000, rms=0.724 (0.038%), neg=0, invalid=766 0114: dt=1.024000, rms=0.723 (0.013%), neg=0, invalid=766 0115: dt=1.024000, rms=0.723 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.723, neg=0, invalid=766 0116: dt=1.024000, rms=0.723 (0.090%), neg=0, invalid=766 0117: dt=0.000000, rms=0.723 (0.002%), neg=0, invalid=766 0118: dt=0.100000, rms=0.723 (-0.008%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.703, neg=0, invalid=766 0119: dt=0.789663, rms=0.687 (2.236%), neg=0, invalid=766 0120: dt=0.028000, rms=0.686 (0.167%), neg=0, invalid=766 0121: dt=0.028000, rms=0.686 (-0.033%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.686, neg=0, invalid=766 0122: dt=0.020000, rms=0.686 (0.030%), neg=0, invalid=766 0123: dt=0.000000, rms=0.686 (-0.002%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13294 (37) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3428 voxels, overlap=0.182) Left_Lateral_Ventricle (4): linear fit = 1.48 x + 0.0 (3428 voxels, peak = 35), gca=35.4 gca peak = 0.14022 (22) mri peak = 0.14668 (36) Right_Lateral_Ventricle (43): linear fit = 1.58 x + 0.0 (2946 voxels, overlap=0.066) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (2946 voxels, peak = 35), gca=33.0 gca peak = 0.24234 (100) mri peak = 0.21124 (105) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (576 voxels, overlap=0.849) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (576 voxels, peak = 105), gca=105.0 gca peak = 0.19192 (97) mri peak = 0.12706 (105) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (539 voxels, overlap=0.728) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (539 voxels, peak = 104), gca=104.3 gca peak = 0.24007 (63) mri peak = 0.13673 (76) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1168 voxels, overlap=0.010) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1168 voxels, peak = 76), gca=75.6 gca peak = 0.29892 (64) mri peak = 0.10735 (80) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1323 voxels, overlap=0.005) Left_Hippocampus (17): linear fit = 1.23 x + 0.0 (1323 voxels, peak = 78), gca=78.4 gca peak = 0.12541 (104) mri peak = 0.06641 (106) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (112251 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (112251 voxels, peak = 109), gca=109.2 gca peak = 0.13686 (104) mri peak = 0.06908 (106) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (116931 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (116931 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.03068 (80) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (67290 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (67290 voxels, peak = 82), gca=81.9 gca peak = 0.13270 (63) mri peak = 0.03152 (84) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (67682 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.33 x + 0.0 (67682 voxels, peak = 83), gca=83.5 gca peak = 0.15182 (70) mri peak = 0.11632 (93) Right_Caudate (50): linear fit = 1.25 x + 0.0 (826 voxels, overlap=0.001) Right_Caudate (50): linear fit = 1.25 x + 0.0 (826 voxels, peak = 88), gca=87.5 gca peak = 0.14251 (76) mri peak = 0.15021 (88) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1066 voxels, overlap=0.058) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1066 voxels, peak = 86), gca=85.5 gca peak = 0.12116 (60) mri peak = 0.04553 (84) Left_Cerebellum_Cortex (8): linear fit = 1.42 x + 0.0 (40198 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.42 x + 0.0 (40198 voxels, peak = 86), gca=85.5 gca peak = 0.12723 (61) mri peak = 0.05371 (78) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (45086 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (45086 voxels, peak = 81), gca=80.8 gca peak = 0.22684 (88) mri peak = 0.08547 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (13319 voxels, overlap=0.476) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (13319 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.12265 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (11754 voxels, overlap=0.617) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (11754 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.17733 (77) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (482 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (482 voxels, peak = 76), gca=76.0 gca peak = 0.39668 (62) mri peak = 0.21331 (77) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (471 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (471 voxels, peak = 76), gca=76.0 gca peak = 0.10129 (93) mri peak = 0.11577 (101) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6275 voxels, overlap=0.752) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (6275 voxels, peak = 98), gca=97.6 gca peak = 0.12071 (89) mri peak = 0.11312 (97) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (5578 voxels, overlap=0.626) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (5578 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.09629 (98) Left_Putamen (12): linear fit = 1.15 x + 0.0 (3130 voxels, overlap=0.128) Left_Putamen (12): linear fit = 1.15 x + 0.0 (3130 voxels, peak = 94), gca=94.3 gca peak = 0.15214 (84) mri peak = 0.09658 (95) Right_Putamen (51): linear fit = 1.12 x + 0.0 (3015 voxels, overlap=0.369) Right_Putamen (51): linear fit = 1.12 x + 0.0 (3015 voxels, peak = 94), gca=94.5 gca peak = 0.08983 (85) mri peak = 0.08818 (92) Brain_Stem (16): linear fit = 1.08 x + 0.0 (16691 voxels, overlap=0.591) Brain_Stem (16): linear fit = 1.08 x + 0.0 (16691 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.08056 (101) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1704 voxels, overlap=0.355) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1704 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.07918 (100) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (2023 voxels, overlap=0.321) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (2023 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.07486 (42) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (125 voxels, overlap=0.834) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (125 voxels, peak = 40), gca=40.5 gca peak = 0.13542 (27) mri peak = 0.11118 (34) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (830 voxels, overlap=0.158) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (830 voxels, peak = 33), gca=33.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) not using caudate to estimate GM means estimating mean gm scale to be 1.25 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.33 x + 0.0 Left_Pallidum too bright - rescaling by 0.983 (from 1.075) to 102.5 (was 104.3) Right_Pallidum too bright - rescaling by 0.976 (from 1.050) to 102.5 (was 105.0) 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=0.654, neg=0, invalid=766 0124: dt=117.119715, rms=0.624 (4.618%), neg=0, invalid=766 0125: dt=259.473904, rms=0.616 (1.281%), neg=0, invalid=766 0126: dt=129.472000, rms=0.612 (0.607%), neg=0, invalid=766 0127: dt=295.936000, rms=0.610 (0.358%), neg=0, invalid=766 0128: dt=129.472000, rms=0.608 (0.436%), neg=0, invalid=766 0129: dt=129.472000, rms=0.607 (0.082%), neg=0, invalid=766 0130: dt=1183.744000, rms=0.602 (0.857%), neg=0, invalid=766 0131: dt=61.235880, rms=0.601 (0.182%), neg=0, invalid=766 0132: dt=32.368000, rms=0.601 (0.013%), neg=0, invalid=766 0133: dt=32.368000, rms=0.601 (0.011%), neg=0, invalid=766 0134: dt=32.368000, rms=0.601 (0.013%), neg=0, invalid=766 0135: dt=32.368000, rms=0.600 (0.024%), neg=0, invalid=766 0136: dt=32.368000, rms=0.600 (0.050%), neg=0, invalid=766 0137: dt=32.368000, rms=0.600 (0.089%), neg=0, invalid=766 0138: dt=32.368000, rms=0.599 (0.119%), neg=0, invalid=766 0139: dt=32.368000, rms=0.598 (0.127%), neg=0, invalid=766 0140: dt=32.368000, rms=0.597 (0.118%), neg=0, invalid=766 0141: dt=32.368000, rms=0.597 (0.105%), neg=0, invalid=766 0142: dt=32.368000, rms=0.596 (0.087%), neg=0, invalid=766 0143: dt=32.368000, rms=0.596 (0.078%), neg=0, invalid=766 0144: dt=32.368000, rms=0.595 (0.069%), neg=0, invalid=766 0145: dt=32.368000, rms=0.595 (0.072%), neg=0, invalid=766 0146: dt=32.368000, rms=0.594 (0.081%), neg=0, invalid=766 0147: dt=32.368000, rms=0.594 (0.098%), neg=0, invalid=766 0148: dt=32.368000, rms=0.593 (0.102%), neg=0, invalid=766 0149: dt=32.368000, rms=0.593 (0.101%), neg=0, invalid=766 0150: dt=32.368000, rms=0.592 (0.092%), neg=0, invalid=766 0151: dt=32.368000, rms=0.592 (0.082%), neg=0, invalid=766 0152: dt=32.368000, rms=0.591 (0.071%), neg=0, invalid=766 0153: dt=32.368000, rms=0.591 (0.062%), neg=0, invalid=766 0154: dt=32.368000, rms=0.591 (0.054%), neg=0, invalid=766 0155: dt=32.368000, rms=0.590 (0.055%), neg=0, invalid=766 0156: dt=32.368000, rms=0.590 (0.060%), neg=0, invalid=766 0157: dt=32.368000, rms=0.590 (0.062%), neg=0, invalid=766 0158: dt=32.368000, rms=0.589 (0.064%), neg=0, invalid=766 0159: dt=32.368000, rms=0.589 (0.062%), neg=0, invalid=766 0160: dt=32.368000, rms=0.588 (0.061%), neg=0, invalid=766 0161: dt=32.368000, rms=0.588 (0.053%), neg=0, invalid=766 0162: dt=32.368000, rms=0.588 (0.048%), neg=0, invalid=766 0163: dt=32.368000, rms=0.588 (0.043%), neg=0, invalid=766 0164: dt=32.368000, rms=0.587 (0.041%), neg=0, invalid=766 0165: dt=32.368000, rms=0.587 (0.041%), neg=0, invalid=766 0166: dt=32.368000, rms=0.587 (0.045%), neg=0, invalid=766 0167: dt=32.368000, rms=0.587 (0.049%), neg=0, invalid=766 0168: dt=32.368000, rms=0.586 (0.053%), neg=0, invalid=766 0169: dt=32.368000, rms=0.586 (0.050%), neg=0, invalid=766 0170: dt=32.368000, rms=0.586 (0.047%), neg=0, invalid=766 0171: dt=32.368000, rms=0.585 (0.041%), neg=0, invalid=766 0172: dt=32.368000, rms=0.585 (0.039%), neg=0, invalid=766 0173: dt=32.368000, rms=0.585 (0.035%), neg=0, invalid=766 0174: dt=32.368000, rms=0.585 (0.035%), neg=0, invalid=766 0175: dt=32.368000, rms=0.585 (0.035%), neg=0, invalid=766 0176: dt=32.368000, rms=0.584 (0.037%), neg=0, invalid=766 0177: dt=32.368000, rms=0.584 (0.040%), neg=0, invalid=766 0178: dt=32.368000, rms=0.584 (0.039%), neg=0, invalid=766 0179: dt=32.368000, rms=0.584 (0.036%), neg=0, invalid=766 0180: dt=32.368000, rms=0.583 (0.035%), neg=0, invalid=766 0181: dt=32.368000, rms=0.583 (0.032%), neg=0, invalid=766 0182: dt=32.368000, rms=0.583 (0.030%), neg=0, invalid=766 0183: dt=32.368000, rms=0.583 (0.030%), neg=0, invalid=766 0184: dt=32.368000, rms=0.583 (0.031%), neg=0, invalid=766 0185: dt=32.368000, rms=0.583 (0.029%), neg=0, invalid=766 0186: dt=32.368000, rms=0.582 (0.031%), neg=0, invalid=766 0187: dt=32.368000, rms=0.582 (0.031%), neg=0, invalid=766 0188: dt=32.368000, rms=0.582 (0.031%), neg=0, invalid=766 0189: dt=32.368000, rms=0.582 (0.031%), neg=0, invalid=766 0190: dt=32.368000, rms=0.582 (0.030%), neg=0, invalid=766 0191: dt=32.368000, rms=0.582 (0.029%), neg=0, invalid=766 0192: dt=32.368000, rms=0.581 (0.028%), neg=0, invalid=766 0193: dt=32.368000, rms=0.581 (0.029%), neg=0, invalid=766 0194: dt=32.368000, rms=0.581 (0.027%), neg=0, invalid=766 0195: dt=32.368000, rms=0.581 (0.028%), neg=0, invalid=766 0196: dt=32.368000, rms=0.581 (0.029%), neg=0, invalid=766 0197: dt=32.368000, rms=0.581 (0.027%), neg=0, invalid=766 0198: dt=32.368000, rms=0.580 (0.026%), neg=0, invalid=766 0199: dt=32.368000, rms=0.580 (0.024%), neg=0, invalid=766 0200: dt=32.368000, rms=0.580 (0.022%), neg=0, invalid=766 0201: dt=2071.552000, rms=0.580 (0.055%), neg=0, invalid=766 0202: dt=129.472000, rms=0.579 (0.108%), neg=0, invalid=766 0203: dt=0.000000, rms=0.579 (-0.001%), neg=0, invalid=766 0204: dt=0.850000, rms=0.579 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.579, neg=0, invalid=766 0205: dt=129.472000, rms=0.578 (0.125%), neg=0, invalid=766 0206: dt=517.888000, rms=0.577 (0.262%), neg=0, invalid=766 0207: dt=27.744000, rms=0.577 (0.004%), neg=0, invalid=766 0208: dt=27.744000, rms=0.577 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.578, neg=0, invalid=766 0209: dt=80.678788, rms=0.575 (0.472%), neg=0, invalid=766 0210: dt=145.152000, rms=0.567 (1.428%), neg=0, invalid=766 0211: dt=43.216495, rms=0.565 (0.460%), neg=0, invalid=766 0212: dt=55.172414, rms=0.563 (0.284%), neg=0, invalid=766 0213: dt=248.832000, rms=0.558 (0.900%), neg=0, invalid=766 0214: dt=83.874145, rms=0.554 (0.697%), neg=0, invalid=766 0215: dt=48.000000, rms=0.553 (0.154%), neg=0, invalid=766 0216: dt=248.832000, rms=0.550 (0.636%), neg=0, invalid=766 0217: dt=37.000000, rms=0.548 (0.227%), neg=0, invalid=766 0218: dt=124.416000, rms=0.547 (0.195%), neg=0, invalid=766 0219: dt=62.208000, rms=0.546 (0.227%), neg=0, invalid=766 0220: dt=36.288000, rms=0.546 (0.067%), neg=0, invalid=766 0221: dt=497.664000, rms=0.543 (0.586%), neg=0, invalid=766 0222: dt=42.666667, rms=0.540 (0.402%), neg=0, invalid=766 0223: dt=20.736000, rms=0.540 (0.016%), neg=0, invalid=766 0224: dt=20.736000, rms=0.540 (0.022%), neg=0, invalid=766 0225: dt=20.736000, rms=0.540 (0.041%), neg=0, invalid=766 0226: dt=20.736000, rms=0.540 (0.065%), neg=0, invalid=766 0227: dt=20.736000, rms=0.539 (0.093%), neg=0, invalid=766 0228: dt=20.736000, rms=0.538 (0.114%), neg=0, invalid=766 0229: dt=20.736000, rms=0.538 (0.119%), neg=0, invalid=766 0230: dt=20.736000, rms=0.537 (0.125%), neg=0, invalid=766 0231: dt=20.736000, rms=0.536 (0.126%), neg=0, invalid=766 0232: dt=20.736000, rms=0.536 (0.134%), neg=0, invalid=766 0233: dt=20.736000, rms=0.535 (0.143%), neg=0, invalid=766 0234: dt=20.736000, rms=0.534 (0.145%), neg=0, invalid=766 0235: dt=20.736000, rms=0.533 (0.140%), neg=0, invalid=766 0236: dt=20.736000, rms=0.533 (0.131%), neg=0, invalid=766 0237: dt=20.736000, rms=0.532 (0.124%), neg=0, invalid=766 0238: dt=20.736000, rms=0.531 (0.126%), neg=0, invalid=766 0239: dt=20.736000, rms=0.531 (0.130%), neg=0, invalid=766 0240: dt=20.736000, rms=0.530 (0.132%), neg=0, invalid=766 0241: dt=20.736000, rms=0.529 (0.132%), neg=0, invalid=766 0242: dt=20.736000, rms=0.529 (0.130%), neg=0, invalid=766 0243: dt=20.736000, rms=0.528 (0.122%), neg=0, invalid=766 0244: dt=20.736000, rms=0.527 (0.117%), neg=0, invalid=766 0245: dt=20.736000, rms=0.527 (0.111%), neg=0, invalid=766 0246: dt=20.736000, rms=0.526 (0.105%), neg=0, invalid=766 0247: dt=20.736000, rms=0.526 (0.102%), neg=0, invalid=766 0248: dt=20.736000, rms=0.525 (0.101%), neg=0, invalid=766 0249: dt=20.736000, rms=0.525 (0.096%), neg=0, invalid=766 0250: dt=20.736000, rms=0.524 (0.089%), neg=0, invalid=766 0251: dt=20.736000, rms=0.524 (0.084%), neg=0, invalid=766 0252: dt=20.736000, rms=0.523 (0.078%), neg=0, invalid=766 0253: dt=20.736000, rms=0.523 (0.077%), neg=0, invalid=766 0254: dt=20.736000, rms=0.523 (0.077%), neg=0, invalid=766 0255: dt=20.736000, rms=0.522 (0.075%), neg=0, invalid=766 0256: dt=20.736000, rms=0.522 (0.073%), neg=0, invalid=766 0257: dt=20.736000, rms=0.521 (0.067%), neg=0, invalid=766 0258: dt=20.736000, rms=0.521 (0.061%), neg=0, invalid=766 0259: dt=20.736000, rms=0.521 (0.062%), neg=0, invalid=766 0260: dt=20.736000, rms=0.520 (0.064%), neg=0, invalid=766 0261: dt=20.736000, rms=0.520 (0.064%), neg=0, invalid=766 0262: dt=20.736000, rms=0.520 (0.059%), neg=0, invalid=766 0263: dt=20.736000, rms=0.520 (0.056%), neg=0, invalid=766 0264: dt=20.736000, rms=0.519 (0.051%), neg=0, invalid=766 0265: dt=20.736000, rms=0.519 (0.048%), neg=0, invalid=766 0266: dt=20.736000, rms=0.519 (0.049%), neg=0, invalid=766 0267: dt=20.736000, rms=0.519 (0.049%), neg=0, invalid=766 0268: dt=20.736000, rms=0.518 (0.045%), neg=0, invalid=766 0269: dt=20.736000, rms=0.518 (0.038%), neg=0, invalid=766 0270: dt=20.736000, rms=0.518 (0.036%), neg=0, invalid=766 0271: dt=20.736000, rms=0.518 (0.037%), neg=0, invalid=766 0272: dt=20.736000, rms=0.517 (0.042%), neg=0, invalid=766 0273: dt=20.736000, rms=0.517 (0.045%), neg=0, invalid=766 0274: dt=20.736000, rms=0.517 (0.039%), neg=0, invalid=766 0275: dt=20.736000, rms=0.517 (0.038%), neg=0, invalid=766 0276: dt=20.736000, rms=0.517 (0.033%), neg=0, invalid=766 0277: dt=20.736000, rms=0.516 (0.037%), neg=0, invalid=766 0278: dt=20.736000, rms=0.516 (0.038%), neg=0, invalid=766 0279: dt=20.736000, rms=0.516 (0.039%), neg=0, invalid=766 0280: dt=20.736000, rms=0.516 (0.032%), neg=0, invalid=766 0281: dt=20.736000, rms=0.516 (0.029%), neg=0, invalid=766 0282: dt=20.736000, rms=0.516 (0.029%), neg=0, invalid=766 0283: dt=20.736000, rms=0.515 (0.029%), neg=0, invalid=766 0284: dt=20.736000, rms=0.515 (0.031%), neg=0, invalid=766 0285: dt=20.736000, rms=0.515 (0.035%), neg=0, invalid=766 0286: dt=20.736000, rms=0.515 (0.032%), neg=0, invalid=766 0287: dt=20.736000, rms=0.515 (0.029%), neg=0, invalid=766 0288: dt=20.736000, rms=0.515 (0.026%), neg=0, invalid=766 0289: dt=20.736000, rms=0.515 (0.027%), neg=0, invalid=766 0290: dt=20.736000, rms=0.514 (0.029%), neg=0, invalid=766 0291: dt=20.736000, rms=0.514 (0.033%), neg=0, invalid=766 0292: dt=20.736000, rms=0.514 (0.030%), neg=0, invalid=766 0293: dt=20.736000, rms=0.514 (0.026%), neg=0, invalid=766 0294: dt=20.736000, rms=0.514 (0.019%), neg=0, invalid=766 0295: dt=20.736000, rms=0.514 (0.018%), neg=0, invalid=766 0296: dt=145.152000, rms=0.514 (0.027%), neg=0, invalid=766 0297: dt=15.552000, rms=0.514 (0.001%), neg=0, invalid=766 0298: dt=15.552000, rms=0.514 (0.001%), neg=0, invalid=766 0299: dt=15.552000, rms=0.514 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.514, neg=0, invalid=766 0300: dt=96.842105, rms=0.512 (0.258%), neg=0, invalid=766 0301: dt=68.541935, rms=0.512 (0.132%), neg=0, invalid=766 0302: dt=39.111111, rms=0.511 (0.049%), neg=0, invalid=766 0303: dt=39.111111, rms=0.511 (0.046%), neg=0, invalid=766 0304: dt=39.111111, rms=0.511 (0.062%), neg=0, invalid=766 0305: dt=39.111111, rms=0.510 (0.068%), neg=0, invalid=766 0306: dt=39.111111, rms=0.510 (0.067%), neg=0, invalid=766 0307: dt=39.111111, rms=0.510 (0.068%), neg=0, invalid=766 0308: dt=39.111111, rms=0.509 (0.061%), neg=0, invalid=766 0309: dt=39.111111, rms=0.509 (0.050%), neg=0, invalid=766 0310: dt=39.111111, rms=0.509 (0.051%), neg=0, invalid=766 0311: dt=39.111111, rms=0.509 (0.049%), neg=0, invalid=766 0312: dt=39.111111, rms=0.508 (0.049%), neg=0, invalid=766 0313: dt=39.111111, rms=0.508 (0.052%), neg=0, invalid=766 0314: dt=39.111111, rms=0.508 (0.048%), neg=0, invalid=766 0315: dt=39.111111, rms=0.508 (0.047%), neg=0, invalid=766 0316: dt=39.111111, rms=0.507 (0.049%), neg=0, invalid=766 0317: dt=39.111111, rms=0.507 (0.039%), neg=0, invalid=766 0318: dt=39.111111, rms=0.507 (0.036%), neg=0, invalid=766 0319: dt=39.111111, rms=0.507 (0.039%), neg=0, invalid=766 0320: dt=39.111111, rms=0.507 (0.047%), neg=0, invalid=766 0321: dt=39.111111, rms=0.506 (0.038%), neg=0, invalid=766 0322: dt=39.111111, rms=0.506 (0.040%), neg=0, invalid=766 0323: dt=39.111111, rms=0.506 (0.043%), neg=0, invalid=766 0324: dt=39.111111, rms=0.506 (0.046%), neg=0, invalid=766 0325: dt=39.111111, rms=0.506 (0.036%), neg=0, invalid=766 0326: dt=39.111111, rms=0.505 (0.026%), neg=0, invalid=766 0327: dt=39.111111, rms=0.505 (0.031%), neg=0, invalid=766 0328: dt=39.111111, rms=0.505 (0.033%), neg=0, invalid=766 0329: dt=39.111111, rms=0.505 (0.026%), neg=0, invalid=766 0330: dt=39.111111, rms=0.505 (0.020%), neg=0, invalid=766 0331: dt=39.111111, rms=0.505 (0.023%), neg=0, invalid=766 0332: dt=39.111111, rms=0.505 (0.038%), neg=0, invalid=766 0333: dt=39.111111, rms=0.504 (0.041%), neg=0, invalid=766 0334: dt=39.111111, rms=0.504 (0.028%), neg=0, invalid=766 0335: dt=39.111111, rms=0.504 (0.025%), neg=0, invalid=766 0336: dt=39.111111, rms=0.504 (0.028%), neg=0, invalid=766 0337: dt=39.111111, rms=0.504 (0.030%), neg=0, invalid=766 0338: dt=39.111111, rms=0.504 (0.031%), neg=0, invalid=766 0339: dt=39.111111, rms=0.504 (0.027%), neg=0, invalid=766 0340: dt=39.111111, rms=0.503 (0.025%), neg=0, invalid=766 0341: dt=39.111111, rms=0.503 (0.032%), neg=0, invalid=766 0342: dt=39.111111, rms=0.503 (0.023%), neg=0, invalid=766 0343: dt=39.111111, rms=0.503 (0.018%), neg=0, invalid=766 0344: dt=145.152000, rms=0.503 (0.016%), neg=0, invalid=766 0345: dt=145.152000, rms=0.503 (-0.124%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=766 0346: dt=22.438247, rms=0.513 (0.201%), neg=0, invalid=766 0347: dt=51.478261, rms=0.512 (0.356%), neg=0, invalid=766 0348: dt=21.857923, rms=0.510 (0.273%), neg=0, invalid=766 0349: dt=30.415842, rms=0.509 (0.261%), neg=0, invalid=766 0350: dt=19.200000, rms=0.508 (0.207%), neg=0, invalid=766 0351: dt=14.545455, rms=0.507 (0.121%), neg=0, invalid=766 0352: dt=44.800000, rms=0.506 (0.251%), neg=0, invalid=766 0353: dt=20.945455, rms=0.505 (0.199%), neg=0, invalid=766 0354: dt=21.090909, rms=0.504 (0.098%), neg=0, invalid=766 0355: dt=32.000000, rms=0.503 (0.209%), neg=0, invalid=766 0356: dt=11.200000, rms=0.503 (0.065%), neg=0, invalid=766 0357: dt=44.800000, rms=0.502 (0.169%), neg=0, invalid=766 0358: dt=25.600000, rms=0.501 (0.176%), neg=0, invalid=766 0359: dt=11.200000, rms=0.501 (0.038%), neg=0, invalid=766 0360: dt=11.200000, rms=0.501 (0.062%), neg=0, invalid=766 0361: dt=11.200000, rms=0.500 (0.087%), neg=0, invalid=766 0362: dt=11.200000, rms=0.500 (0.131%), neg=0, invalid=766 0363: dt=11.200000, rms=0.499 (0.146%), neg=0, invalid=766 0364: dt=11.200000, rms=0.498 (0.159%), neg=0, invalid=766 0365: dt=11.200000, rms=0.497 (0.176%), neg=0, invalid=766 0366: dt=11.200000, rms=0.496 (0.193%), neg=0, invalid=766 0367: dt=11.200000, rms=0.495 (0.191%), neg=0, invalid=766 0368: dt=11.200000, rms=0.495 (0.170%), neg=0, invalid=766 0369: dt=11.200000, rms=0.494 (0.157%), neg=0, invalid=766 0370: dt=11.200000, rms=0.493 (0.161%), neg=0, invalid=766 0371: dt=11.200000, rms=0.492 (0.158%), neg=0, invalid=766 0372: dt=11.200000, rms=0.492 (0.139%), neg=0, invalid=766 0373: dt=11.200000, rms=0.491 (0.142%), neg=0, invalid=766 0374: dt=11.200000, rms=0.490 (0.142%), neg=0, invalid=766 0375: dt=11.200000, rms=0.489 (0.140%), neg=0, invalid=766 0376: dt=11.200000, rms=0.489 (0.124%), neg=0, invalid=766 0377: dt=11.200000, rms=0.488 (0.107%), neg=0, invalid=766 0378: dt=11.200000, rms=0.488 (0.102%), neg=0, invalid=766 0379: dt=11.200000, rms=0.487 (0.100%), neg=0, invalid=766 0380: dt=11.200000, rms=0.487 (0.095%), neg=0, invalid=766 0381: dt=11.200000, rms=0.486 (0.082%), neg=0, invalid=766 0382: dt=11.200000, rms=0.486 (0.075%), neg=0, invalid=766 0383: dt=11.200000, rms=0.486 (0.072%), neg=0, invalid=766 0384: dt=11.200000, rms=0.485 (0.069%), neg=0, invalid=766 0385: dt=11.200000, rms=0.485 (0.059%), neg=0, invalid=766 0386: dt=11.200000, rms=0.485 (0.056%), neg=0, invalid=766 0387: dt=11.200000, rms=0.485 (0.054%), neg=0, invalid=766 0388: dt=11.200000, rms=0.484 (0.050%), neg=0, invalid=766 0389: dt=11.200000, rms=0.484 (0.039%), neg=0, invalid=766 0390: dt=11.200000, rms=0.484 (0.035%), neg=0, invalid=766 0391: dt=11.200000, rms=0.484 (0.033%), neg=0, invalid=766 0392: dt=11.200000, rms=0.484 (0.033%), neg=0, invalid=766 0393: dt=11.200000, rms=0.484 (0.030%), neg=0, invalid=766 0394: dt=11.200000, rms=0.483 (0.032%), neg=0, invalid=766 0395: dt=11.200000, rms=0.483 (0.034%), neg=0, invalid=766 0396: dt=11.200000, rms=0.483 (0.033%), neg=0, invalid=766 0397: dt=11.200000, rms=0.483 (0.030%), neg=0, invalid=766 0398: dt=11.200000, rms=0.483 (0.023%), neg=0, invalid=766 0399: dt=11.200000, rms=0.483 (0.022%), neg=0, invalid=766 0400: dt=25.600000, rms=0.483 (0.009%), neg=0, invalid=766 0401: dt=25.600000, rms=0.483 (-0.006%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.483, neg=0, invalid=766 0402: dt=44.261682, rms=0.481 (0.321%), neg=0, invalid=766 0403: dt=14.095238, rms=0.481 (0.099%), neg=0, invalid=766 0404: dt=44.800000, rms=0.480 (0.072%), neg=0, invalid=766 0405: dt=11.294118, rms=0.480 (0.042%), neg=0, invalid=766 0406: dt=11.294118, rms=0.480 (0.017%), neg=0, invalid=766 0407: dt=11.294118, rms=0.480 (0.028%), neg=0, invalid=766 0408: dt=11.294118, rms=0.480 (0.037%), neg=0, invalid=766 0409: dt=11.294118, rms=0.480 (0.035%), neg=0, invalid=766 0410: dt=11.294118, rms=0.479 (0.034%), neg=0, invalid=766 0411: dt=11.294118, rms=0.479 (0.019%), neg=0, invalid=766 0412: dt=11.294118, rms=0.479 (0.016%), neg=0, invalid=766 0413: dt=19.200000, rms=0.479 (0.006%), neg=0, invalid=766 0414: dt=19.200000, rms=0.479 (0.025%), neg=0, invalid=766 0415: dt=19.200000, rms=0.479 (0.009%), neg=0, invalid=766 0416: dt=19.200000, rms=0.479 (0.036%), neg=0, invalid=766 0417: dt=19.200000, rms=0.479 (0.034%), neg=0, invalid=766 0418: dt=19.200000, rms=0.479 (0.037%), neg=0, invalid=766 0419: dt=19.200000, rms=0.478 (0.033%), neg=0, invalid=766 0420: dt=19.200000, rms=0.478 (0.035%), neg=0, invalid=766 0421: dt=19.200000, rms=0.478 (0.033%), neg=0, invalid=766 0422: dt=19.200000, rms=0.478 (0.032%), neg=0, invalid=766 0423: dt=19.200000, rms=0.478 (0.032%), neg=0, invalid=766 0424: dt=19.200000, rms=0.478 (0.039%), neg=0, invalid=766 0425: dt=19.200000, rms=0.477 (0.021%), neg=0, invalid=766 0426: dt=19.200000, rms=0.477 (0.033%), neg=0, invalid=766 0427: dt=19.200000, rms=0.477 (0.031%), neg=0, invalid=766 0428: dt=19.200000, rms=0.477 (0.017%), neg=0, invalid=766 0429: dt=19.200000, rms=0.477 (0.039%), neg=0, invalid=766 0430: dt=19.200000, rms=0.477 (0.026%), neg=0, invalid=766 0431: dt=19.200000, rms=0.477 (0.024%), neg=0, invalid=766 0432: dt=19.200000, rms=0.476 (0.046%), neg=0, invalid=766 0433: dt=19.200000, rms=0.476 (0.024%), neg=0, invalid=766 0434: dt=19.200000, rms=0.476 (0.018%), neg=0, invalid=766 0435: dt=25.600000, rms=0.476 (0.011%), neg=0, invalid=766 0436: dt=25.600000, rms=0.476 (-0.011%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.499, neg=0, invalid=766 0437: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.499, neg=0, invalid=766 0438: dt=0.000000, rms=0.499 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.545, neg=0, invalid=766 0439: dt=1.536000, rms=0.540 (0.911%), neg=0, invalid=766 0440: dt=0.479167, rms=0.539 (0.057%), neg=0, invalid=766 0441: dt=0.320000, rms=0.539 (0.012%), neg=0, invalid=766 0442: dt=0.320000, rms=0.539 (-0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.539, neg=0, invalid=766 0443: dt=0.950617, rms=0.539 (0.104%), neg=0, invalid=766 0444: dt=0.384000, rms=0.539 (0.009%), neg=0, invalid=766 0445: dt=0.384000, rms=0.539 (-0.003%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.493, neg=0, invalid=766 0446: dt=0.448000, rms=0.481 (2.510%), neg=0, invalid=766 0447: dt=0.320000, rms=0.479 (0.344%), neg=0, invalid=766 0448: dt=0.320000, rms=0.478 (0.269%), neg=0, invalid=766 0449: dt=0.384000, rms=0.477 (0.247%), neg=0, invalid=766 0450: dt=0.028000, rms=0.477 (0.015%), neg=0, invalid=766 0451: dt=0.028000, rms=0.477 (0.013%), neg=0, invalid=766 0452: dt=0.028000, rms=0.477 (0.025%), neg=0, invalid=766 0453: dt=0.028000, rms=0.476 (0.035%), neg=0, invalid=766 0454: dt=0.028000, rms=0.476 (0.043%), neg=0, invalid=766 0455: dt=0.028000, rms=0.476 (0.049%), neg=0, invalid=766 0456: dt=0.028000, rms=0.476 (0.054%), neg=0, invalid=766 0457: dt=0.028000, rms=0.475 (0.057%), neg=0, invalid=766 0458: dt=0.028000, rms=0.475 (0.061%), neg=0, invalid=766 0459: dt=0.028000, rms=0.475 (0.061%), neg=0, invalid=766 0460: dt=0.028000, rms=0.475 (0.062%), neg=0, invalid=766 0461: dt=0.028000, rms=0.474 (0.059%), neg=0, invalid=766 0462: dt=0.028000, rms=0.474 (0.058%), neg=0, invalid=766 0463: dt=0.028000, rms=0.474 (0.055%), neg=0, invalid=766 0464: dt=0.028000, rms=0.474 (0.054%), neg=0, invalid=766 0465: dt=0.028000, rms=0.473 (0.050%), neg=0, invalid=766 0466: dt=0.028000, rms=0.473 (0.046%), neg=0, invalid=766 0467: dt=0.028000, rms=0.473 (0.043%), neg=0, invalid=766 0468: dt=0.028000, rms=0.473 (0.038%), neg=0, invalid=766 0469: dt=0.028000, rms=0.473 (0.035%), neg=0, invalid=766 0470: dt=0.028000, rms=0.472 (0.031%), neg=0, invalid=766 0471: dt=0.028000, rms=0.472 (0.028%), neg=0, invalid=766 0472: dt=0.028000, rms=0.472 (0.025%), neg=0, invalid=766 0473: dt=0.028000, rms=0.472 (0.021%), neg=0, invalid=766 0474: dt=0.028000, rms=0.472 (0.020%), neg=0, invalid=766 0475: dt=0.000000, rms=0.472 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.472, neg=0, invalid=766 0476: dt=0.448000, rms=0.469 (0.660%), neg=0, invalid=766 0477: dt=0.081221, rms=0.469 (0.007%), neg=0, invalid=766 0478: dt=0.081221, rms=0.469 (0.006%), neg=0, invalid=766 0479: dt=0.081221, rms=0.469 (0.009%), neg=0, invalid=766 0480: dt=0.081221, rms=0.469 (0.004%), neg=0, invalid=766 0481: dt=0.081221, rms=0.469 (0.007%), neg=0, invalid=766 0482: dt=0.081221, rms=0.469 (0.009%), neg=0, invalid=766 0483: dt=0.081221, rms=0.469 (0.009%), neg=0, invalid=766 0484: dt=0.096000, rms=0.469 (0.002%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.466, neg=0, invalid=766 0485: dt=0.000000, rms=0.467 (-0.089%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0486: dt=110.976000, rms=0.466 (0.054%), neg=0, invalid=766 0487: dt=295.936000, rms=0.466 (0.068%), neg=0, invalid=766 0488: dt=110.976000, rms=0.466 (0.058%), neg=0, invalid=766 0489: dt=55.488000, rms=0.466 (0.006%), neg=0, invalid=766 0490: dt=55.488000, rms=0.466 (0.008%), neg=0, invalid=766 0491: dt=55.488000, rms=0.466 (0.014%), neg=0, invalid=766 0492: dt=55.488000, rms=0.466 (0.019%), neg=0, invalid=766 0493: dt=55.488000, rms=0.466 (0.022%), neg=0, invalid=766 0494: dt=55.488000, rms=0.465 (0.022%), neg=0, invalid=766 0495: dt=55.488000, rms=0.465 (0.020%), neg=0, invalid=766 0496: dt=55.488000, rms=0.465 (0.017%), neg=0, invalid=766 0497: dt=517.888000, rms=0.465 (0.018%), neg=0, invalid=766 0498: dt=129.472000, rms=0.465 (0.017%), neg=0, invalid=766 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=766 0499: dt=20.736000, rms=0.465 (0.037%), neg=0, invalid=766 0500: dt=25.920000, rms=0.465 (0.019%), neg=0, invalid=766 0501: dt=25.920000, rms=0.465 (0.027%), neg=0, invalid=766 0502: dt=25.920000, rms=0.465 (0.021%), neg=0, invalid=766 0503: dt=25.920000, rms=0.465 (-0.004%), neg=0, invalid=766 0504: dt=145.152000, rms=0.464 (0.163%), neg=0, invalid=766 0505: dt=36.288000, rms=0.464 (0.022%), neg=0, invalid=766 0506: dt=1.134000, rms=0.464 (0.001%), neg=0, invalid=766 0507: dt=0.070875, rms=0.464 (0.000%), neg=0, invalid=766 0508: dt=0.035437, rms=0.464 (0.000%), neg=0, invalid=766 0509: dt=0.030375, rms=0.464 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0510: dt=0.008859, rms=0.464 (0.000%), neg=0, invalid=766 0511: dt=0.004860, rms=0.464 (0.000%), neg=0, invalid=766 0512: dt=0.000304, rms=0.464 (0.000%), neg=0, invalid=766 0513: dt=0.000152, rms=0.464 (0.000%), neg=0, invalid=766 0514: dt=0.000038, rms=0.464 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0515: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=766 0516: dt=0.000000, rms=0.464 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=766 0517: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=766 0518: dt=0.000000, rms=0.465 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.467, neg=0, invalid=766 0519: dt=0.112000, rms=0.467 (0.077%), neg=0, invalid=766 0520: dt=0.112000, rms=0.467 (0.075%), neg=0, invalid=766 0521: dt=1.536000, rms=0.462 (0.938%), neg=0, invalid=766 0522: dt=0.448000, rms=0.462 (0.137%), neg=0, invalid=766 0523: dt=1.792000, rms=0.459 (0.473%), neg=0, invalid=766 0524: dt=1.792000, rms=0.458 (0.207%), neg=0, invalid=766 0525: dt=1.792000, rms=0.458 (0.147%), neg=0, invalid=766 0526: dt=0.112000, rms=0.458 (0.006%), neg=0, invalid=766 0527: dt=0.112000, rms=0.458 (0.004%), neg=0, invalid=766 0528: dt=0.112000, rms=0.458 (0.008%), neg=0, invalid=766 0529: dt=0.112000, rms=0.458 (0.012%), neg=0, invalid=766 0530: dt=0.112000, rms=0.458 (0.016%), neg=0, invalid=766 0531: dt=0.112000, rms=0.457 (0.018%), neg=0, invalid=766 0532: dt=0.112000, rms=0.457 (0.020%), neg=0, invalid=766 0533: dt=0.112000, rms=0.457 (0.022%), neg=0, invalid=766 0534: dt=0.112000, rms=0.457 (0.023%), neg=0, invalid=766 0535: dt=0.112000, rms=0.457 (0.023%), neg=0, invalid=766 0536: dt=0.112000, rms=0.457 (0.023%), neg=0, invalid=766 0537: dt=0.112000, rms=0.457 (0.021%), neg=0, invalid=766 0538: dt=1.792000, rms=0.457 (0.015%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.457, neg=0, invalid=766 0539: dt=1.792000, rms=0.455 (0.408%), neg=0, invalid=766 0540: dt=1.792000, rms=0.454 (0.218%), neg=0, invalid=766 0541: dt=0.500000, rms=0.454 (0.041%), neg=0, invalid=766 0542: dt=0.500000, rms=0.454 (0.037%), neg=0, invalid=766 0543: dt=0.500000, rms=0.453 (0.066%), neg=0, invalid=766 0544: dt=0.500000, rms=0.453 (0.084%), neg=0, invalid=766 0545: dt=0.500000, rms=0.453 (0.092%), neg=0, invalid=766 0546: dt=0.500000, rms=0.452 (0.092%), neg=0, invalid=766 0547: dt=0.500000, rms=0.452 (0.086%), neg=0, invalid=766 0548: dt=0.500000, rms=0.451 (0.078%), neg=0, invalid=766 0549: dt=0.500000, rms=0.451 (0.069%), neg=0, invalid=766 0550: dt=0.500000, rms=0.451 (0.060%), neg=0, invalid=766 0551: dt=0.500000, rms=0.451 (0.051%), neg=0, invalid=766 0552: dt=0.500000, rms=0.450 (0.042%), neg=0, invalid=766 0553: dt=0.500000, rms=0.450 (0.033%), neg=0, invalid=766 0554: dt=0.500000, rms=0.450 (-0.000%), neg=0, invalid=766 0555: dt=0.001250, rms=0.450 (0.000%), neg=0, invalid=766 0556: dt=0.000030, rms=0.450 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.446, neg=0, invalid=766 0557: dt=0.028000, rms=0.446 (0.146%), neg=0, invalid=766 0558: dt=0.028000, rms=0.445 (0.137%), neg=0, invalid=766 0559: dt=0.028000, rms=0.444 (0.129%), neg=0, invalid=766 0560: dt=0.028000, rms=0.444 (0.122%), neg=0, invalid=766 0561: dt=0.028000, rms=0.443 (0.114%), neg=0, invalid=766 0562: dt=0.122549, rms=0.441 (0.466%), neg=0, invalid=766 0563: dt=0.112000, rms=0.440 (0.318%), neg=0, invalid=766 0564: dt=0.028000, rms=0.440 (0.063%), neg=0, invalid=766 0565: dt=0.028000, rms=0.439 (0.060%), neg=0, invalid=766 0566: dt=0.028000, rms=0.439 (0.057%), neg=0, invalid=766 0567: dt=0.112000, rms=0.438 (0.215%), neg=0, invalid=766 0568: dt=0.028000, rms=0.438 (0.043%), neg=0, invalid=766 0569: dt=0.028000, rms=0.438 (0.041%), neg=0, invalid=766 0570: dt=0.028000, rms=0.438 (0.039%), neg=0, invalid=766 0571: dt=0.028000, rms=0.437 (0.073%), neg=0, invalid=766 0572: dt=0.028000, rms=0.437 (0.099%), neg=0, invalid=766 0573: dt=0.028000, rms=0.437 (0.029%), neg=0, invalid=766 0574: dt=0.028000, rms=0.436 (0.055%), neg=0, invalid=766 0575: dt=0.028000, rms=0.436 (0.075%), neg=0, invalid=766 0576: dt=0.028000, rms=0.436 (0.023%), neg=0, invalid=766 0577: dt=0.028000, rms=0.436 (0.043%), neg=0, invalid=766 0578: dt=0.028000, rms=0.436 (0.058%), neg=0, invalid=766 0579: dt=0.028000, rms=0.435 (0.070%), neg=0, invalid=766 0580: dt=0.028000, rms=0.435 (0.015%), neg=0, invalid=766 0581: dt=0.014000, rms=0.435 (0.007%), neg=0, invalid=766 0582: dt=0.028000, rms=0.435 (0.015%), neg=0, invalid=766 0583: dt=0.096000, rms=0.435 (0.049%), neg=0, invalid=766 0584: dt=0.112000, rms=0.435 (0.050%), neg=0, invalid=766 0585: dt=0.007000, rms=0.435 (0.003%), neg=0, invalid=766 0586: dt=0.007000, rms=0.435 (0.003%), neg=0, invalid=766 0587: dt=0.007000, rms=0.435 (0.003%), neg=0, invalid=766 0588: dt=0.007000, rms=0.435 (0.005%), neg=0, invalid=766 0589: dt=0.007000, rms=0.435 (0.007%), neg=0, invalid=766 0590: dt=0.007000, rms=0.435 (0.009%), neg=0, invalid=766 0591: dt=0.007000, rms=0.435 (0.011%), neg=0, invalid=766 0592: dt=0.007000, rms=0.435 (0.002%), neg=0, invalid=766 0593: dt=0.080000, rms=0.434 (0.028%), neg=0, invalid=766 0594: dt=0.028000, rms=0.434 (0.009%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.434, neg=0, invalid=766 0595: dt=0.007000, rms=0.434 (0.013%), neg=0, invalid=766 0596: dt=0.024000, rms=0.434 (0.044%), neg=0, invalid=766 0597: dt=0.080000, rms=0.434 (0.138%), neg=0, invalid=766 0598: dt=0.028000, rms=0.433 (0.040%), neg=0, invalid=766 0599: dt=0.028000, rms=0.433 (0.037%), neg=0, invalid=766 0600: dt=0.028000, rms=0.433 (0.035%), neg=0, invalid=766 0601: dt=0.014000, rms=0.433 (0.017%), neg=0, invalid=766 0602: dt=0.014000, rms=0.433 (0.031%), neg=0, invalid=766 0603: dt=0.014000, rms=0.433 (0.042%), neg=0, invalid=766 0604: dt=0.014000, rms=0.432 (0.051%), neg=0, invalid=766 0605: dt=0.014000, rms=0.432 (0.058%), neg=0, invalid=766 0606: dt=0.014000, rms=0.432 (0.061%), neg=0, invalid=766 0607: dt=0.014000, rms=0.432 (0.063%), neg=0, invalid=766 0608: dt=0.014000, rms=0.431 (0.062%), neg=0, invalid=766 0609: dt=0.014000, rms=0.431 (0.060%), neg=0, invalid=766 0610: dt=0.014000, rms=0.431 (0.057%), neg=0, invalid=766 0611: dt=0.014000, rms=0.431 (0.053%), neg=0, invalid=766 0612: dt=0.014000, rms=0.431 (0.001%), neg=0, invalid=766 0613: dt=0.014000, rms=0.431 (0.001%), neg=0, invalid=766 0614: dt=0.014000, rms=0.431 (0.003%), neg=0, invalid=766 0615: dt=0.014000, rms=0.431 (0.004%), neg=0, invalid=766 0616: dt=0.014000, rms=0.431 (0.005%), neg=0, invalid=766 0617: dt=0.014000, rms=0.431 (0.006%), neg=0, invalid=766 0618: dt=0.014000, rms=0.431 (0.006%), neg=0, invalid=766 0619: dt=0.014000, rms=0.430 (0.007%), neg=0, invalid=766 0620: dt=0.014000, rms=0.430 (0.008%), neg=0, invalid=766 0621: dt=0.014000, rms=0.430 (0.008%), neg=0, invalid=766 0622: dt=0.014000, rms=0.430 (0.009%), neg=0, invalid=766 0623: dt=0.014000, rms=0.430 (0.001%), neg=0, invalid=766 0624: dt=0.028000, rms=0.430 (0.003%), neg=0, invalid=766 0625: dt=0.112000, rms=0.430 (0.011%), neg=0, invalid=766 0626: dt=0.028000, rms=0.430 (0.003%), neg=0, invalid=766 0627: dt=0.028000, rms=0.430 (0.003%), neg=0, invalid=766 0628: dt=0.028000, rms=0.430 (0.002%), neg=0, invalid=766 0629: dt=0.014000, rms=0.430 (0.001%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... registration took 6 hours, 16 minutes and 9 seconds. #-------------------------------------- #@# CA Reg Inv Fri Jun 19 20:11:57 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Fri Jun 19 20:13:02 CEST 2009 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 10898531 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 19 seconds. #-------------------------------------- #@# SkullLTA Fri Jun 19 20:14:21 CEST 2009 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.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 '/usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 using (102, 93, 120) as brain centroid... mean wm in atlas = 126, using box (81,70,93) --> (122, 116,147) to find MRI wm before smoothing, mri peak at 100 after smoothing, mri peak at 99, scaling input intensities by 1.273 scaling channel 0 by 1.27273 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-16244.7, old_max_log_p =-14346.0 (thresh=-14331.6) 1.041 -0.153 -0.018 13.573; 0.147 1.246 0.164 -62.155; 0.002 -0.131 1.013 10.530; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16148.1, old_max_log_p =-16244.7 (thresh=-16228.5) 1.057 -0.155 -0.018 11.875; 0.147 1.246 0.164 -62.155; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16103.3, old_max_log_p =-16148.1 (thresh=-16131.9) 1.040 -0.153 -0.018 13.654; 0.147 1.246 0.164 -62.155; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-16103.3, old_max_log_p =-16103.3 (thresh=-16087.1) 1.040 -0.153 -0.018 13.654; 0.147 1.246 0.164 -62.155; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-16095.0, old_max_log_p =-16103.3 (thresh=-16087.1) 1.040 -0.153 -0.018 13.654; 0.148 1.251 0.165 -63.340; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04025 -0.15275 -0.01788 13.65427; 0.14792 1.25050 0.16479 -63.34011; 0.00220 -0.13341 1.02876 7.16317; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.04025 -0.15275 -0.01788 13.65427; 0.14792 1.25050 0.16479 -63.34011; 0.00220 -0.13341 1.02876 7.16317; 0.00000 0.00000 0.00000 1.00000; v3p/netlib/opt/lbfgs.c: lb3_1.lp > 0 outof QuasiNewtonEMA: 005: -log(p) = 16095.0 tol 0.000010 Resulting transform: 1.040 -0.153 -0.018 13.654; 0.148 1.251 0.165 -63.340; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -16095.0 (old=-14346.0) transform before final EM align: 1.040 -0.153 -0.018 13.654; 0.148 1.251 0.165 -63.340; 0.002 -0.133 1.029 7.163; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.04025 -0.15275 -0.01788 13.65427; 0.14792 1.25050 0.16479 -63.34011; 0.00220 -0.13341 1.02876 7.16317; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.04025 -0.15275 -0.01788 13.65427; 0.14792 1.25050 0.16479 -63.34011; 0.00220 -0.13341 1.02876 7.16317; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 004: -log(p) = 2076465.0 after pass:transform: ( 1.04, -0.15, -0.02, 13.65) ( 0.16, 1.25, 0.17, -63.34) ( 0.00, -0.13, 1.02, 7.16) 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: 006: -log(p) = 2076465.0 tol 0.000000 final transform: 1.039 -0.152 -0.019 13.654; 0.158 1.254 0.175 -63.340; 0.001 -0.134 1.023 7.163; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 10 minutes and 48 seconds. #-------------------------------------- #@# SubCort Seg Fri Jun 19 20:25:09 CEST 2009 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /usr/local/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.16281 (37) Left_Lateral_Ventricle (4): linear fit = 1.35 x + 0.0 (2732 voxels, overlap=0.081) Left_Lateral_Ventricle (4): linear fit = 1.35 x + 0.0 (2732 voxels, peak = 36), gca=36.5 gca peak = 0.14982 (20) mri peak = 0.16514 (36) Right_Lateral_Ventricle (43): linear fit = 1.65 x + 0.0 (3090 voxels, overlap=0.067) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (3090 voxels, peak = 33), gca=30.0 gca peak = 0.28003 (97) mri peak = 0.27236 (105) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (352 voxels, overlap=0.518) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (352 voxels, peak = 104), gca=104.3 gca peak = 0.18160 (96) mri peak = 0.18323 (106) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (464 voxels, overlap=0.132) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (464 voxels, peak = 103), gca=103.2 gca peak = 0.27536 (62) mri peak = 0.11770 (77) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1259 voxels, overlap=0.000) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (1259 voxels, peak = 74), gca=74.4 gca peak = 0.32745 (63) mri peak = 0.10438 (80) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1353 voxels, overlap=0.000) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1353 voxels, peak = 76), gca=75.6 gca peak = 0.08597 (105) mri peak = 0.07523 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (73222 voxels, overlap=0.608) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (73222 voxels, peak = 110), gca=110.2 gca peak = 0.09209 (106) mri peak = 0.07767 (109) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (89167 voxels, overlap=0.600) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (89167 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04302 (84) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (73386 voxels, overlap=0.038) Left_Cerebral_Cortex (3): linear fit = 1.30 x + 0.0 (73386 voxels, peak = 82), gca=81.9 gca peak = 0.08598 (64) mri peak = 0.04213 (84) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (74712 voxels, overlap=0.074) Right_Cerebral_Cortex (42): linear fit = 1.30 x + 0.0 (74712 voxels, peak = 83), gca=83.2 gca peak = 0.24164 (71) mri peak = 0.17626 (93) Right_Caudate (50): linear fit = 1.27 x + 0.0 (975 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.27 x + 0.0 (975 voxels, peak = 91), gca=90.5 gca peak = 0.18227 (75) mri peak = 0.18163 (88) Left_Caudate (11): linear fit = 1.17 x + 0.0 (953 voxels, overlap=0.058) Left_Caudate (11): linear fit = 1.17 x + 0.0 (953 voxels, peak = 88), gca=88.1 gca peak = 0.10629 (62) mri peak = 0.06457 (84) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (39333 voxels, overlap=0.000) Left_Cerebellum_Cortex (8): linear fit = 1.40 x + 0.0 (39333 voxels, peak = 87), gca=86.8 gca peak = 0.11668 (59) mri peak = 0.06774 (78) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (42549 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (42549 voxels, peak = 78), gca=78.2 gca peak = 0.17849 (88) mri peak = 0.10583 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7647 voxels, overlap=0.251) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7647 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.15025 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7026 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (7026 voxels, peak = 90), gca=90.3 gca peak = 0.41688 (64) mri peak = 0.16336 (80) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (648 voxels, overlap=0.000) Left_Amygdala (18): linear fit = 1.23 x + 0.0 (648 voxels, peak = 78), gca=78.4 gca peak = 0.42394 (62) mri peak = 0.15715 (77) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (671 voxels, overlap=0.000) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (671 voxels, peak = 74), gca=74.4 gca peak = 0.10041 (96) mri peak = 0.12315 (101) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5398 voxels, overlap=0.774) Left_Thalamus_Proper (10): linear fit = 1.05 x + 0.0 (5398 voxels, peak = 101), gca=100.8 gca peak = 0.13978 (88) mri peak = 0.12547 (97) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5702 voxels, overlap=0.484) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (5702 voxels, peak = 97), gca=96.8 gca peak = 0.08514 (81) mri peak = 0.11646 (99) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1982 voxels, overlap=0.186) Left_Putamen (12): linear fit = 1.15 x + 0.0 (1982 voxels, peak = 93), gca=93.2 gca peak = 0.09624 (82) mri peak = 0.13424 (94) Right_Putamen (51): linear fit = 1.15 x + 0.0 (1784 voxels, overlap=0.254) Right_Putamen (51): linear fit = 1.15 x + 0.0 (1784 voxels, peak = 94), gca=94.3 gca peak = 0.07543 (88) mri peak = 0.08697 (92) Brain_Stem (16): linear fit = 1.05 x + 0.0 (17395 voxels, overlap=0.687) Brain_Stem (16): linear fit = 1.05 x + 0.0 (17395 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.10279 (101) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1784 voxels, overlap=0.393) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1784 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.11179 (102) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1975 voxels, overlap=0.330) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1975 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.11778 (42) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (87 voxels, overlap=0.852) Third_Ventricle (14): linear fit = 1.12 x + 0.0 (87 voxels, peak = 40), gca=40.5 gca peak = 0.26069 (23) mri peak = 0.19270 (34) Fourth_Ventricle (15): linear fit = 1.45 x + 0.0 (318 voxels, overlap=0.147) Fourth_Ventricle (15): linear fit = 1.45 x + 0.0 (318 voxels, peak = 33), gca=33.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.24 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 1.36 x + 0.0 Right_Pallidum too bright - rescaling by 0.997 (from 1.075) to 104.0 (was 104.3) renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.13655 (37) mri peak = 0.16281 (37) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2732 voxels, overlap=0.597) Left_Lateral_Ventricle (4): linear fit = 1.00 x + 0.0 (2732 voxels, peak = 37), gca=37.0 gca peak = 0.12220 (30) mri peak = 0.16514 (36) Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (3090 voxels, overlap=0.474) Right_Lateral_Ventricle (43): linear fit = 1.15 x + 0.0 (3090 voxels, peak = 34), gca=34.5 gca peak = 0.26657 (97) mri peak = 0.27236 (105) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (352 voxels, overlap=0.452) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (352 voxels, peak = 104), gca=104.3 gca peak = 0.17636 (104) mri peak = 0.18323 (106) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (464 voxels, overlap=0.720) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (464 voxels, peak = 104), gca=104.0 gca peak = 0.23622 (75) mri peak = 0.11770 (77) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1259 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1259 voxels, peak = 75), gca=75.0 gca peak = 0.26057 (76) mri peak = 0.10438 (80) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1353 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1353 voxels, peak = 76), gca=76.0 gca peak = 0.08006 (112) mri peak = 0.07523 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (73222 voxels, overlap=0.772) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (73222 voxels, peak = 112), gca=112.0 gca peak = 0.08548 (108) mri peak = 0.07767 (109) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (89167 voxels, overlap=0.676) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (89167 voxels, peak = 108), gca=108.0 gca peak = 0.05850 (82) mri peak = 0.04302 (84) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (73386 voxels, overlap=0.820) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (73386 voxels, peak = 82), gca=82.0 gca peak = 0.06789 (82) mri peak = 0.04213 (84) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (74712 voxels, overlap=0.865) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (74712 voxels, peak = 82), gca=82.0 gca peak = 0.23913 (94) mri peak = 0.17626 (93) Right_Caudate (50): linear fit = 1.00 x + 0.0 (975 voxels, overlap=0.986) Right_Caudate (50): linear fit = 1.00 x + 0.0 (975 voxels, peak = 94), gca=94.0 gca peak = 0.16562 (88) mri peak = 0.18163 (88) Left_Caudate (11): linear fit = 1.00 x + 0.0 (953 voxels, overlap=0.608) Left_Caudate (11): linear fit = 1.00 x + 0.0 (953 voxels, peak = 88), gca=88.0 gca peak = 0.08223 (87) mri peak = 0.06457 (84) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (39333 voxels, overlap=0.903) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (39333 voxels, peak = 87), gca=87.0 gca peak = 0.09519 (79) mri peak = 0.06774 (78) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42549 voxels, overlap=0.929) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (42549 voxels, peak = 79), gca=79.0 gca peak = 0.17137 (94) mri peak = 0.10583 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7647 voxels, overlap=0.936) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (7647 voxels, peak = 96), gca=96.3 gca peak = 0.16003 (91) mri peak = 0.15025 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7026 voxels, overlap=0.944) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7026 voxels, peak = 91), gca=91.0 gca peak = 0.32067 (78) mri peak = 0.16336 (80) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (648 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (648 voxels, peak = 78), gca=78.0 gca peak = 0.34135 (75) mri peak = 0.15715 (77) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (671 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (671 voxels, peak = 75), gca=75.0 gca peak = 0.10157 (99) mri peak = 0.12315 (101) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5398 voxels, overlap=0.932) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (5398 voxels, peak = 99), gca=99.0 gca peak = 0.10139 (97) mri peak = 0.12547 (97) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5702 voxels, overlap=0.763) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5702 voxels, peak = 97), gca=97.0 gca peak = 0.08609 (93) mri peak = 0.11646 (99) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1982 voxels, overlap=0.781) Left_Putamen (12): linear fit = 1.00 x + 0.0 (1982 voxels, peak = 93), gca=93.0 gca peak = 0.09065 (87) mri peak = 0.13424 (94) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1784 voxels, overlap=0.665) Right_Putamen (51): linear fit = 1.00 x + 0.0 (1784 voxels, peak = 87), gca=87.0 gca peak = 0.07207 (90) mri peak = 0.08697 (92) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17395 voxels, overlap=0.774) Brain_Stem (16): linear fit = 1.00 x + 0.0 (17395 voxels, peak = 90), gca=90.0 gca peak = 0.12275 (98) mri peak = 0.10279 (101) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1784 voxels, overlap=0.762) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1784 voxels, peak = 98), gca=98.0 gca peak = 0.15957 (99) mri peak = 0.11179 (102) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1975 voxels, overlap=0.795) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1975 voxels, peak = 99), gca=99.0 gca peak = 0.16754 (41) mri peak = 0.11778 (42) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (87 voxels, overlap=0.999) Third_Ventricle (14): linear fit = 0.98 x + 0.0 (87 voxels, peak = 40), gca=40.0 gca peak = 0.16462 (34) mri peak = 0.19270 (34) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (318 voxels, overlap=0.565) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (318 voxels, peak = 33), gca=33.2 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26961 (42) gca peak CSF = 0.17120 (52) gca peak Left_Accumbens_area = 0.50212 (82) gca peak Left_undetermined = 0.95107 (42) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.08662 (41) gca peak Right_Inf_Lat_Vent = 0.28322 (38) gca peak Right_Accumbens_area = 0.26412 (92) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.13262 (46) gca peak Fifth_Ventricle = 0.46296 (56) gca peak WM_hypointensities = 0.14285 (85) gca peak non_WM_hypointensities = 0.10331 (55) gca peak Optic_Chiasm = 0.34124 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.02 x + 0.0 Left_Pallidum too bright - rescaling by 1.005 (from 1.000) to 104.5 (was 104.0) Right_Pallidum too bright - rescaling by 1.002 (from 1.075) to 104.5 (was 104.3) 53331 gm and wm labels changed (%35 to gray, %65 to white out of all changed labels) 483 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 80991 changed. image ll: -2.187, PF=1.000 pass 2: 15275 changed. image ll: -2.184, PF=1.000 pass 3: 6219 changed. pass 4: 2954 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 28 minutes and 27 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz 1005 reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz reading aseg from /data/MOODS2/freesurfer/1005/mri/aseg.auto_noCCseg.mgz reading norm from /data/MOODS2/freesurfer/1005/mri/norm.mgz 73555 voxels in left wm, 91980 in right wm, xrange [116, 132] global minimum found at slice 129.0, rotations (-2.00, 7.25) final transformation (x=129.0, yr=-2.000, zr=7.250): 0.991 -0.126 -0.035 20.694; 0.126 0.992 -0.004 -14.683; 0.035 0.000 0.999 -4.424; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 121 91 eigenvectors: -0.001 0.002 1.000; 0.007 -1.000 0.002; 1.000 0.007 0.001; error in mid anterior detected - correcting... writing aseg with callosum to to /data/MOODS2/freesurfer/1005/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.6 minutes cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Jun 19 20:56:12 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 55404 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 2 minutes and 34 seconds. using MR volume brainmask.mgz to mask input volume... using wm (106) threshold 96.0 for removing exterior voxels white matter peak found at 111 gm peak at 88 (88), valley at 54 (54) csf peak at 19, setting threshold to 65 white matter peak found at 111 gm peak at 88 (88), valley at 54 (54) csf peak at 19, setting threshold to 65 #-------------------------------------------- #@# Mask BFS Fri Jun 19 20:58:50 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Jun 19 20:58:54 CEST 2009 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 103.2 +- 5.8 [80.0 --> 125.0] GM (82.0) : 78.9 +- 12.6 [30.0 --> 96.0] setting bottom of white matter range to 91.5 setting top of gray matter range to 102.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4260 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3941 filled 2294 bright non-wm voxels segmented. 2972 diagonally connected voxels added... white matter segmentation took 2.0 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 0.96 minutes reading wm segmentation from wm.seg.mgz... 622 voxels added to wm to prevent paths from MTL structures to cortex 2489 additional wm voxels added 0 additional wm voxels added SEG EDIT: 45499 voxels turned on, 61133 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 41 found - 41 modified | TOTAL: 41 pass 2 (xy+): 0 found - 41 modified | TOTAL: 41 pass 1 (xy-): 42 found - 42 modified | TOTAL: 83 pass 2 (xy-): 0 found - 42 modified | TOTAL: 83 pass 1 (yz+): 49 found - 49 modified | TOTAL: 132 pass 2 (yz+): 0 found - 49 modified | TOTAL: 132 pass 1 (yz-): 39 found - 39 modified | TOTAL: 171 pass 2 (yz-): 0 found - 39 modified | TOTAL: 171 pass 1 (xz+): 25 found - 25 modified | TOTAL: 196 pass 2 (xz+): 0 found - 25 modified | TOTAL: 196 pass 1 (xz-): 42 found - 42 modified | TOTAL: 238 pass 2 (xz-): 0 found - 42 modified | TOTAL: 238 Iteration Number : 1 pass 1 (+++): 25 found - 25 modified | TOTAL: 25 pass 2 (+++): 0 found - 25 modified | TOTAL: 25 pass 1 (+++): 18 found - 18 modified | TOTAL: 43 pass 2 (+++): 0 found - 18 modified | TOTAL: 43 pass 1 (+++): 17 found - 17 modified | TOTAL: 60 pass 2 (+++): 0 found - 17 modified | TOTAL: 60 pass 1 (+++): 19 found - 19 modified | TOTAL: 79 pass 2 (+++): 0 found - 19 modified | TOTAL: 79 Iteration Number : 1 pass 1 (++): 67 found - 67 modified | TOTAL: 67 pass 2 (++): 0 found - 67 modified | TOTAL: 67 pass 1 (+-): 40 found - 40 modified | TOTAL: 107 pass 2 (+-): 0 found - 40 modified | TOTAL: 107 pass 1 (--): 82 found - 82 modified | TOTAL: 189 pass 2 (--): 0 found - 82 modified | TOTAL: 189 pass 1 (-+): 45 found - 45 modified | TOTAL: 234 pass 2 (-+): 0 found - 45 modified | TOTAL: 234 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 6 found - 6 modified | TOTAL: 9 pass 2 (xy-): 0 found - 6 modified | TOTAL: 9 pass 1 (yz+): 4 found - 4 modified | TOTAL: 13 pass 2 (yz+): 0 found - 4 modified | TOTAL: 13 pass 1 (yz-): 4 found - 4 modified | TOTAL: 17 pass 2 (yz-): 0 found - 4 modified | TOTAL: 17 pass 1 (xz+): 4 found - 4 modified | TOTAL: 21 pass 2 (xz+): 0 found - 4 modified | TOTAL: 21 pass 1 (xz-): 2 found - 2 modified | TOTAL: 23 pass 2 (xz-): 0 found - 2 modified | TOTAL: 23 Iteration Number : 2 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 4 found - 4 modified | TOTAL: 12 pass 2 (+++): 0 found - 4 modified | TOTAL: 12 pass 1 (+++): 0 found - 0 modified | TOTAL: 12 Iteration Number : 2 pass 1 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 4 found - 4 modified | TOTAL: 6 pass 2 (+-): 0 found - 4 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 3 found - 3 modified | TOTAL: 10 pass 2 (-+): 0 found - 3 modified | TOTAL: 10 Iteration Number : 3 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 2 found - 2 modified | TOTAL: 4 pass 2 (xy-): 0 found - 2 modified | TOTAL: 4 pass 1 (yz+): 0 found - 0 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 600 (out of 660650: 0.090820) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Jun 19 21:02:00 CEST 2009 /data/MOODS2/freesurfer/1005/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.792; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.041 -0.153 -0.018 13.573; 0.131 1.107 0.146 -41.792; 0.002 -0.125 0.960 15.483; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1478 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) need search nearby using seed (125, 114, 89), TAL = (3.0, -39.0, 14.0) talairach voxel to voxel transform 0.944 0.130 -0.002 -7.345; -0.110 0.873 -0.135 40.052; -0.016 0.113 1.024 -10.911; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 114, 89) --> (3.0, -39.0, 14.0) done. writing output to filled.mgz... filling took 0.9 minutes talairach cc position changed to (3.00, -39.00, 14.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, -39.00, 14.00) SRC: (108.33, 115.85, 91.34) search lh wm seed point around talairach space (-15.00, -39.00, 14.00), SRC: (142.32, 111.91, 90.76) 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 Fri Jun 19 21:02:52 CEST 2009 /data/MOODS2/freesurfer/1005/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 2 found - 2 modified | TOTAL: 3 pass 2 (yz-): 0 found - 2 modified | TOTAL: 3 pass 1 (xz+): 1 found - 1 modified | TOTAL: 4 pass 2 (xz+): 0 found - 1 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 319080: 0.001567) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ slice 30: 822 vertices, 921 faces slice 40: 5693 vertices, 5899 faces slice 50: 13932 vertices, 14247 faces slice 60: 23840 vertices, 24205 faces slice 70: 34817 vertices, 35226 faces slice 80: 45461 vertices, 45849 faces slice 90: 56718 vertices, 57168 faces slice 100: 69703 vertices, 70195 faces slice 110: 82937 vertices, 83440 faces slice 120: 95246 vertices, 95700 faces slice 130: 107340 vertices, 107821 faces slice 140: 118228 vertices, 118642 faces slice 150: 126859 vertices, 127244 faces slice 160: 135211 vertices, 135589 faces slice 170: 142456 vertices, 142764 faces slice 180: 148199 vertices, 148464 faces slice 190: 152191 vertices, 152386 faces slice 200: 153596 vertices, 153682 faces slice 210: 153596 vertices, 153682 faces slice 220: 153596 vertices, 153682 faces slice 230: 153596 vertices, 153682 faces slice 240: 153596 vertices, 153682 faces slice 250: 153596 vertices, 153682 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 153596 voxel in cpt #1: X=-86 [v=153596,e=461046,f=307364] located at (-26.028666, -22.515879, 24.929529) For the whole surface: X=-86 [v=153596,e=461046,f=307364] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Jun 19 21:03:08 CEST 2009 mris_smooth -nw ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /data/MOODS2/freesurfer/1005/scripts smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Jun 19 21:03:14 CEST 2009 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /data/MOODS2/freesurfer/1005/scripts avg radius = 48.4 mm, total surface area = 81663 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.5 minutes Not saving sulc step 000: RMS=0.101 (target=0.015) step 005: RMS=0.076 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.049 (target=0.015) step 020: RMS=0.045 (target=0.015) step 025: RMS=0.041 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.034 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.032 (target=0.015) step 060: RMS=0.032 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Jun 19 21:04:43 CEST 2009 /data/MOODS2/freesurfer/1005/scripts mris_sphere -q ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... tol=1.0e+00, sigma=0.0, host=impsy, 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 0.94 +- 0.56 (0.00-->6.72) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.23-->0.92) tol=1.0e-01, sigma=0.0, host=impsy, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization tol=1.8e+01, sigma=0.0, host=impsy, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 301: dt: 236.31, sse: 8035.3 (0.020, 19.6, 0.000), neg: 6787 (%0.332:%0.59), avgs: 32 302: dt: 0.29, sse: 8035.3 (0.020, 19.6, 0.000), neg: 6787 (%0.332:%0.59), avgs: 32 303: dt: 0.29, sse: 8035.2 (0.020, 19.6, 0.000), neg: 6789 (%0.331:%0.59), avgs: 32 304: dt: 0.29, sse: 8035.2 (0.020, 19.6, 0.000), neg: 6794 (%0.331:%0.59), avgs: 32 305: dt: 0.29, sse: 8035.1 (0.020, 19.6, 0.000), neg: 6796 (%0.330:%0.59), avgs: 32 306: dt: 0.29, sse: 8035.1 (0.020, 19.6, 0.000), neg: 6794 (%0.330:%0.59), avgs: 32 307: dt: 0.29, sse: 8035.0 (0.020, 19.6, 0.000), neg: 6794 (%0.329:%0.59), avgs: 32 308: dt: 0.29, sse: 8035.0 (0.020, 19.6, 0.000), neg: 6789 (%0.329:%0.59), avgs: 32 309: dt: 0.29, sse: 8034.9 (0.020, 19.6, 0.000), neg: 6789 (%0.328:%0.59), avgs: 32 310: dt: 0.29, sse: 8034.9 (0.020, 19.6, 0.000), neg: 6784 (%0.327:%0.59), avgs: 32 vertex spacing 0.94 +- 0.56 (0.00-->6.81) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.13-->0.95) 311: dt: 0.29, sse: 8034.9 (0.020, 19.6, 0.000), neg: 6780 (%0.326:%0.59), avgs: 32 312: dt: 298.67, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6680 (%0.245:%0.55), avgs: 32 vertex spacing 0.94 +- 0.56 (0.00-->6.93) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.10-->0.99) 313: dt: 0.00, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6680 (%0.245:%0.55), avgs: 8 314: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6678 (%0.244:%0.55), avgs: 8 315: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6679 (%0.244:%0.55), avgs: 8 316: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6676 (%0.243:%0.55), avgs: 8 317: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6679 (%0.243:%0.55), avgs: 8 318: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6680 (%0.242:%0.55), avgs: 8 319: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6685 (%0.242:%0.55), avgs: 8 320: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6686 (%0.241:%0.55), avgs: 8 vertex spacing 0.94 +- 0.56 (0.00-->6.94) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.09-->0.99) 321: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6697 (%0.241:%0.55), avgs: 8 322: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6699 (%0.240:%0.55), avgs: 8 323: dt: 0.15, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6698 (%0.239:%0.54), avgs: 8 324: dt: 0.00, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6698 (%0.239:%0.54), avgs: 8 vertex spacing 0.94 +- 0.56 (0.00-->6.95) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.09-->0.99) 325: dt: 0.00, sse: 8033.9 (0.020, 19.6, 0.000), neg: 6698 (%0.239:%0.54), avgs: 2 326: dt: 0.09, sse: 8034.0 (0.020, 19.6, 0.000), neg: 6704 (%0.239:%0.54), avgs: 2 327: dt: 0.09, sse: 8034.0 (0.020, 19.6, 0.000), neg: 6707 (%0.238:%0.54), avgs: 2 328: dt: 0.09, sse: 8034.0 (0.020, 19.6, 0.000), neg: 6718 (%0.237:%0.54), avgs: 2 329: dt: 0.09, sse: 8034.0 (0.020, 19.6, 0.000), neg: 6729 (%0.235:%0.54), avgs: 2 330: dt: 0.09, sse: 8034.0 (0.020, 19.6, 0.000), neg: 6747 (%0.234:%0.54), avgs: 2 vertex spacing 0.94 +- 0.56 (0.00-->6.95) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.09-->1.00) 331: dt: 0.09, sse: 8034.1 (0.020, 19.6, 0.000), neg: 6756 (%0.233:%0.54), avgs: 2 332: dt: 0.09, sse: 8034.1 (0.020, 19.6, 0.000), neg: 6772 (%0.232:%0.54), avgs: 2 333: dt: 0.09, sse: 8034.1 (0.020, 19.6, 0.000), neg: 6786 (%0.231:%0.54), avgs: 2 334: dt: 0.09, sse: 8034.2 (0.020, 19.6, 0.000), neg: 6812 (%0.229:%0.54), avgs: 2 335: dt: 0.09, sse: 8034.2 (0.020, 19.6, 0.000), neg: 6825 (%0.228:%0.54), avgs: 2 336: dt: 0.00, sse: 8034.2 (0.020, 19.6, 0.000), neg: 6825 (%0.228:%0.54), avgs: 2 vertex spacing 0.94 +- 0.56 (0.00-->6.97) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.07-->1.00) 337: dt: 0.00, sse: 8034.2 (0.020, 19.6, 0.000), neg: 6825 (%0.228:%0.54), avgs: 0 vertex spacing 0.94 +- 0.56 (0.00-->6.97) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.07-->1.00) tol=1.8e+01, sigma=0.0, host=impsy, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 338: dt: 644.56, sse: 1140.7 (0.020, 19.6, 0.000), neg: 7326 (%0.209:%0.51), avgs: 32 scaling brain by 0.292... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.343, avgs=0 005/300: dt: 0.9000, rms radial error=177.083, avgs=0 010/300: dt: 0.9000, rms radial error=176.523, avgs=0 015/300: dt: 0.9000, rms radial error=175.788, avgs=0 020/300: dt: 0.9000, rms radial error=174.951, avgs=0 025/300: dt: 0.9000, rms radial error=174.056, avgs=0 030/300: dt: 0.9000, rms radial error=173.129, avgs=0 035/300: dt: 0.9000, rms radial error=172.186, avgs=0 040/300: dt: 0.9000, rms radial error=171.235, avgs=0 045/300: dt: 0.9000, rms radial error=170.282, avgs=0 050/300: dt: 0.9000, rms radial error=169.329, avgs=0 055/300: dt: 0.9000, rms radial error=168.379, avgs=0 060/300: dt: 0.9000, rms radial error=167.433, avgs=0 065/300: dt: 0.9000, rms radial error=166.491, avgs=0 070/300: dt: 0.9000, rms radial error=165.553, avgs=0 075/300: dt: 0.9000, rms radial error=164.620, avgs=0 080/300: dt: 0.9000, rms radial error=163.691, avgs=0 085/300: dt: 0.9000, rms radial error=162.768, avgs=0 090/300: dt: 0.9000, rms radial error=161.850, avgs=0 095/300: dt: 0.9000, rms radial error=160.936, avgs=0 100/300: dt: 0.9000, rms radial error=160.028, avgs=0 105/300: dt: 0.9000, rms radial error=159.124, avgs=0 110/300: dt: 0.9000, rms radial error=158.225, avgs=0 115/300: dt: 0.9000, rms radial error=157.331, avgs=0 120/300: dt: 0.9000, rms radial error=156.442, avgs=0 125/300: dt: 0.9000, rms radial error=155.558, avgs=0 130/300: dt: 0.9000, rms radial error=154.680, avgs=0 135/300: dt: 0.9000, rms radial error=153.809, avgs=0 140/300: dt: 0.9000, rms radial error=152.945, avgs=0 145/300: dt: 0.9000, rms radial error=152.085, avgs=0 150/300: dt: 0.9000, rms radial error=151.230, avgs=0 155/300: dt: 0.9000, rms radial error=150.379, avgs=0 160/300: dt: 0.9000, rms radial error=149.534, avgs=0 165/300: dt: 0.9000, rms radial error=148.692, avgs=0 170/300: dt: 0.9000, rms radial error=147.856, avgs=0 175/300: dt: 0.9000, rms radial error=147.024, avgs=0 180/300: dt: 0.9000, rms radial error=146.197, avgs=0 185/300: dt: 0.9000, rms radial error=145.374, avgs=0 190/300: dt: 0.9000, rms radial error=144.556, avgs=0 195/300: dt: 0.9000, rms radial error=143.742, avgs=0 200/300: dt: 0.9000, rms radial error=142.933, avgs=0 205/300: dt: 0.9000, rms radial error=142.129, avgs=0 210/300: dt: 0.9000, rms radial error=141.328, avgs=0 215/300: dt: 0.9000, rms radial error=140.533, avgs=0 220/300: dt: 0.9000, rms radial error=139.741, avgs=0 225/300: dt: 0.9000, rms radial error=138.954, avgs=0 230/300: dt: 0.9000, rms radial error=138.172, avgs=0 235/300: dt: 0.9000, rms radial error=137.394, avgs=0 240/300: dt: 0.9000, rms radial error=136.620, avgs=0 245/300: dt: 0.9000, rms radial error=135.851, avgs=0 250/300: dt: 0.9000, rms radial error=135.085, avgs=0 255/300: dt: 0.9000, rms radial error=134.325, avgs=0 260/300: dt: 0.9000, rms radial error=133.568, avgs=0 265/300: dt: 0.9000, rms radial error=132.816, avgs=0 270/300: dt: 0.9000, rms radial error=132.067, avgs=0 275/300: dt: 0.9000, rms radial error=131.324, avgs=0 280/300: dt: 0.9000, rms radial error=130.584, avgs=0 285/300: dt: 0.9000, rms radial error=129.848, avgs=0 290/300: dt: 0.9000, rms radial error=129.117, avgs=0 295/300: dt: 0.9000, rms radial error=128.389, avgs=0 300/300: dt: 0.9000, rms radial error=127.666, avgs=0 spherical inflation complete. epoch 1 (K=20.0), pass 1, starting sse = 8038.93 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 = 0.00/37 = 0.00002 epoch 2 (K=80.0), pass 1, starting sse = 1143.59 integrating with navgs=32 and tol=3.200e+00 taking m339: dt: 0.29, sse: 1140.7 (0.020, 19.6, 0.000), neg: 7338 (%0.209:%0.51), avgs: 32 340: dt: 0.29, sse: 1140.7 (0.020, 19.6, 0.000), neg: 7352 (%0.208:%0.51), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->6.99) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.06-->1.01) 341: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7362 (%0.207:%0.51), avgs: 32 342: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7368 (%0.207:%0.51), avgs: 32 343: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7371 (%0.206:%0.51), avgs: 32 344: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7382 (%0.206:%0.51), avgs: 32 345: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7386 (%0.205:%0.51), avgs: 32 346: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7393 (%0.205:%0.51), avgs: 32 347: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7394 (%0.204:%0.51), avgs: 32 348: dt: 0.29, sse: 1140.8 (0.020, 19.6, 0.000), neg: 7392 (%0.203:%0.51), avgs: 32 349: dt: 308.71, sse: 1139.3 (0.020, 19.6, 0.000), neg: 7175 (%0.168:%0.47), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->7.01) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.06-->1.01) 350: dt: 25.37, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7244 (%0.150:%0.45), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.01) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.06-->1.02) 351: dt: 0.15, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7247 (%0.150:%0.45), avgs: 8 352: dt: 0.15, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7252 (%0.150:%0.45), avgs: 8 353: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7252 (%0.150:%0.45), avgs: 8 354: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7260 (%0.150:%0.45), avgs: 8 355: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7266 (%0.150:%0.45), avgs: 8 356: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7272 (%0.150:%0.45), avgs: 8 357: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7274 (%0.150:%0.45), avgs: 8 358: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7280 (%0.150:%0.45), avgs: 8 359: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7277 (%0.150:%0.45), avgs: 8 360: dt: 0.15, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7284 (%0.150:%0.45), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.02) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.07-->1.02) 361: dt: 55.33, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7424 (%0.138:%0.44), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.02) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) 362: dt: 0.00, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7424 (%0.138:%0.44), avgs: 2 363: dt: 0.09, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7430 (%0.138:%0.44), avgs: 2 364: dt: 0.09, sse: 1138.9 (0.020, 19.6, 0.000), neg: 7434 (%0.138:%0.44), avgs: 2 365: dt: 0.09, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7448 (%0.138:%0.44), avgs: 2 366: dt: 0.09, sse: 1139.0 (0.020, 19.6, 0.000), neg: 7459 (%0.137:%0.44), avgs: 2 367: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7469 (%0.137:%0.44), avgs: 2 368: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7477 (%0.137:%0.44), avgs: 2 369: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7489 (%0.137:%0.44), avgs: 2 370: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7500 (%0.137:%0.44), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) 371: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7506 (%0.136:%0.44), avgs: 2 372: dt: 0.09, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7511 (%0.136:%0.44), avgs: 2 373: dt: 0.00, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7511 (%0.136:%0.44), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) 374: dt: 0.00, sse: 1139.0 (0.020, 19.7, 0.000), neg: 7511 (%0.136:%0.44), avgs: 0 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) tol=1.8e+01, sigma=0.0, host=impsy, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 375: dt: 491.37, sse: 102.1 (0.020, 19.5, 0.000), neg: 7445 (%0.119:%0.45), avgs: 32 376: dt: 0.29, sse: 102.1 (0.020, 19.5, 0.000), neg: 7448 (%0.119:%0.45), avgs: 32 377: dt: 0.29, sse: 102.1 (0.020, 19.5, 0.000), neg: 7446 (%0.118:%0.45), avgs: 32 378: dt: 0.29, sse: 102.1 (0.020, 19.5, 0.000), neg: 7447 (%0.118:%0.45), avgs: 32 379: dt: 0.29, sse: 102.1 (0.020, 19.5, 0.000), neg: 7449 (%0.118:%0.45), avgs: 32 380: dt: 0.29, sse: 102.1 (0.020, 19.5, 0.000), neg: 7451 (%0.118:%0.45), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->7.02) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.06-->1.02) 381: dt: 0.29, sse: 102.0 (0.020, 19.5, 0.000), neg: 7450 (%0.118:%0.45), avgs: 32 382: dt: 0.29, sse: 102.0 (0.020, 19.5, 0.000), neg: 7450 (%0.117:%0.45), avgs: 32 383: dt: 0.29, sse: 102.0 (0.020, 19.5, 0.000), neg: 7445 (%0.117:%0.45), avgs: 32 384: dt: 0.29, sse: 102.0 (0.020, 19.5, 0.000), neg: 7447 (%0.117:%0.44), avgs: 32 385: dt: 0.29, sse: 102.0 (0.020, 19.5, 0.000), neg: 7452 (%0.116:%0.44), avgs: 32 386: dt: 94.46, sse: 101.4 (0.020, 19.5, 0.000), neg: 7468 (%0.108:%0.41), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->7.02) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.06-->1.02) 387: dt: 30.79, sse: 101.1 (0.020, 19.5, 0.000), neg: 7438 (%0.103:%0.40), avgs: 8 388: dt: 0.15, sse: 101.0 (0.020, 19.5, 0.000), neg: 7446 (%0.103:%0.40), avgs: 8 389: dt: 0.15, sse: 101.0 (0.020, 19.5, 0.000), neg: 7449 (%0.103:%0.40), avgs: 8 390: dt: 0.15, sse: 101.0 (0.020, 19.5, 0.000), neg: 7443 (%0.102:%0.40), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) 391: dt: 0.15, sse: 101.0 (0.020, 19.5, 0.000), neg: 7446 (%0.102:%0.40), avgs: 8 392: dt: 0.15, sse: 101.0 (0.020, 19.5, 0.000), neg: 7438 (%0.102:%0.40), avgs: 8 393: dt: 0.15, sse: 101.0 (0.020, 19.4, 0.000), neg: 7442 (%0.102:%0.39), avgs: 8 394: dt: 0.15, sse: 101.0 (0.020, 19.4, 0.000), neg: 7438 (%0.102:%0.39), avgs: 8 395: dt: 0.15, sse: 101.0 (0.020, 19.4, 0.000), neg: 7446 (%0.102:%0.39), avgs: 8 396: dt: 0.15, sse: 101.0 (0.020, 19.4, 0.000), neg: 7443 (%0.102:%0.39), avgs: 8 397: dt: 0.15, sse: 101.0 (0.020, 19.4, 0.000), neg: 7443 (%0.102:%0.39), avgs: 8 398: dt: 61.14, sse: 100.6 (0.020, 19.4, 0.000), neg: 7419 (%0.100:%0.40), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.06-->1.02) 399: dt: 3.11, sse: 100.4 (0.020, 19.4, 0.000), neg: 7458 (%0.097:%0.39), avgs: 2 400: dt: 0.09, sse: 100.4 (0.020, 19.4, 0.000), neg: 7463 (%0.097:%0.39), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 110410 --> 110411) face area 0.02 +- 0.03 (-0.05-->1.02) 401: dt: 0.09, sse: 100.4 (0.020, 19.4, 0.000), neg: 7463 (%0.097:%0.39), avgs: 2 402: dt: 0.09, sse: 100.4 (0.020, 19.4, 0.000), neg: 7461 (%0.097:%0.39), avgs: 2 403: dt: 0.09, sse: 100.3 (0.020, 19.4, 0.000), neg: 7466 (%0.096:%0.39), avgs: 2 404: dt: 0.09, sse: 100.3 (0.020, 19.4, 0.000), neg: 7471 (%0.096:%0.39), avgs: 2 405: dt: 0.09, sse: 100.3 (0.020, 19.4, 0.000), neg: 7476 (%0.095:%0.39), avgs: 2 406: dt: 0.09, sse: 100.2 (0.020, 19.4, 0.000), neg: 7484 (%0.095:%0.39), avgs: 2 407: dt: 0.09, sse: 100.2 (0.020, 19.4, 0.000), neg: 7483 (%0.094:%0.39), avgs: 2 408: dt: 0.09, sse: 100.2 (0.020, 19.4, 0.000), neg: 7488 (%0.094:%0.39), avgs: 2 409: dt: 0.09, sse: 100.1 (0.020, 19.4, 0.000), neg: 7484 (%0.094:%0.39), avgs: 2 410: dt: 10.54, sse: 99.8 (0.020, 19.4, 0.000), neg: 7527 (%0.091:%0.39), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 411: dt: 0.17, sse: 99.8 (0.020, 19.4, 0.000), neg: 7565 (%0.090:%0.39), avgs: 0 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) tol=1.8e+01, sigma=0.0, host=impsy, nav=32, nbrs=1, l_nlarea=1.000 using quadratic fit line minimization 412: dt: 68.16, sse: 13.1 (0.020, 19.4, 0.000), neg: 7484 (%0.086:%0.38), avgs: 32 413: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7482 (%0.086:%0.38), avgs: 32 414: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7478 (%0.086:%0.38), avgs: 32 415: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7475 (%0.086:%0.38), avgs: 32 416: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7476 (%0.086:%0.38), avgs: 32 417: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7480 (%0.086:%0.38), avgs: 32 418: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7482 (%0.086:%0.38), avgs: 32 419: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7482 (%0.086:%0.38), avgs: 32 420: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7473 (%0.086:%0.38), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 421: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7468 (%0.086:%0.38), avgs: 32 422: dt: 0.29, sse: 13.1 (0.020, 19.3, 0.000), neg: 7468 (%0.086:%0.38), avgs: 32 423: dt: 93.57, sse: 12.9 (0.020, 19.3, 0.000), neg: 7442 (%0.084:%0.38), avgs: 32 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 424: dt: 39.42, sse: 12.7 (0.020, 19.3, 0.000), neg: 7321 (%0.080:%0.37), avgs: 8 425: dt: 3.63, sse: 12.6 (0.020, 19.3, 0.000), neg: 7339 (%0.078:%0.37), avgs: 8 426: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7333 (%0.078:%0.37), avgs: 8 427: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7336 (%0.078:%0.37), avgs: 8 428: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7332 (%0.077:%0.37), avgs: 8 429: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7331 (%0.077:%0.37), avgs: 8 430: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7330 (%0.077:%0.37), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 431: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7334 (%0.077:%0.37), avgs: 8 432: dt: 0.15, sse: 12.6 (0.020, 19.3, 0.000), neg: 7338 (%0.077:%0.37), avgs: 8 433: dt: 0.15, sse: 12.5 (0.020, 19.3, 0.000), neg: 7341 (%0.077:%0.37), avgs: 8 434: dt: 0.15, sse: 12.5 (0.020, 19.3, 0.000), neg: 7341 (%0.077:%0.37), avgs: 8 435: dt: 0.15, sse: 12.5 (0.020, 19.3, 0.000), neg: 7332 (%0.077:%0.37), avgs: 8 436: dt: 40.60, sse: 12.4 (0.020, 19.3, 0.000), neg: 7253 (%0.074:%0.35), avgs: 8 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 437: dt: 3.89, sse: 12.2 (0.020, 19.2, 0.000), neg: 7249 (%0.071:%0.35), avgs: 2 438: dt: 1.48, sse: 12.1 (0.020, 19.2, 0.000), neg: 7249 (%0.070:%0.34), avgs: 2 439: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7248 (%0.070:%0.34), avgs: 2 440: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7248 (%0.070:%0.34), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.04-->1.02) 441: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7256 (%0.069:%0.35), avgs: 2 442: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7258 (%0.069:%0.35), avgs: 2 443: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7264 (%0.069:%0.35), avgs: 2 444: dt: 0.09, sse: 12.1 (0.020, 19.2, 0.000), neg: 7251 (%0.069:%0.34), avgs: 2 445: dt: 0.09, sse: 12.0 (0.020, 19.2, 0.000), neg: 7247 (%0.069:%0.34), avgs: 2 446: dt: 0.09, sse: 12.0 (0.020, 19.2, 0.000), neg: 7248 (%0.068:%0.34), avgs: 2 447: dt: 0.09, sse: 12.0 (0.020, 19.2, 0.000), neg: 7261 (%0.068:%0.35), avgs: 2 448: dt: 0.09, sse: 12.0 (0.020, 19.2, 0.000), neg: 7259 (%0.068:%0.35), avgs: 2 449: dt: 0.82, sse: 12.0 (0.020, 19.2, 0.000), neg: 7254 (%0.067:%0.35), avgs: 2 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.03-->1.02) 450: dt: 0.52, sse: 11.9 (0.020, 19.2, 0.000), neg: 7243 (%0.066:%0.35), avgs: 0 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.02-->1.02) 451: dt: 0.00, sse: 11.9 (0.020, 19.2, 0.000), neg: 7243 (%0.066:%0.35), avgs: 0 vertex spacing 0.94 +- 0.57 (0.00-->7.03) (max @ vno 73136 --> 74361) face area 0.02 +- 0.03 (-0.02-->1.02) 451: dt: 0.00, sse: 8038.2 (0.020, 19.2, 0.000), neg: 7243 (%0.066:%0.35), avgs: 32 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.26 hours omentum 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 = 0.00/37 = 0.00011 epoch 3 (K=320.0), pass 1, starting sse = 103.71 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 = 0.04/37 = 0.00103 epoch 4 (K=1280.0), pass 1, starting sse = 13.29 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 = 0.11/40 = 0.00265 final distance error %100000.00 optimization complete. unfolding took 0.20 hours #-------------------------------------------- #@# Fix Topology lh Fri Jun 19 21:20:04 CEST 2009 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /data/MOODS2/freesurfer/1005/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga 1005 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 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ before topology correction, eno=-86 (nv=153596, nf=307364, ne=461046, g=44) 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... 14872 ambiguous faces found in tessellation segmenting defects... 31 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 8 -merging segment 18 into 17 29 defects to be corrected 0 vertices coincident reading input surface /data/MOODS2/freesurfer/1005/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.4264 (-4.2132) -vertex loglikelihood: -5.2506 (-2.6253) -normal dot loglikelihood: -3.5695 (-3.5695) -quad curv loglikelihood: -6.3101 (-3.1551) Total Loglikelihood : -23.5567 CORRECTING DEFECT 0 (vertices=254, convex hull=174) After retessellation of defect 0, euler #=-24 (145395,434545,289126) : difference with theory (-26) = -2 CORRECTING DEFECT 1 (vertices=1647, convex hull=345) After retessellation of defect 1, euler #=-24 (145466,434954,289464) : difference with theory (-25) = -1 CORRECTING DEFECT 2 (vertices=150, convex hull=181) After retessellation of defect 2, euler #=-23 (145521,435208,289664) : difference with theory (-24) = -1 CORRECTING DEFECT 3 (vertices=66, convex hull=91) After retessellation of defect 3, euler #=-22 (145554,435346,289770) : difference with theory (-23) = -1 CORRECTING DEFECT 4 (vertices=50, convex hull=42) After retessellation of defect 4, euler #=-21 (145563,435388,289804) : difference with theory (-22) = -1 CORRECTING DEFECT 5 (vertices=23, convex hull=52) After retessellation of defect 5, euler #=-20 (145576,435447,289851) : difference with theory (-21) = -1 CORRECTING DEFECT 6 (vertices=1796, convex hull=524) After retessellation of defect 6, euler #=-19 (145590,435750,290141) : difference with theory (-20) = -1 CORRECTING DEFECT 7 (vertices=31, convex hull=64) After retessellation of defect 7, euler #=-18 (145610,435833,290205) : difference with theory (-19) = -1 CORRECTING DEFECT 8 (vertices=493, convex hull=204) After retessellation of defect 8, euler #=-16 (145633,436002,290353) : difference with theory (-18) = -2 CORRECTING DEFECT 9 (vertices=27, convex hull=60) After retessellation of defect 9, euler #=-15 (145649,436069,290405) : difference with theory (-17) = -2 CORRECTING DEFECT 10 (vertices=39, convex hull=66) After retessellation of defect 10, euler #=-14 (145670,436157,290473) : difference with theory (-16) = -2 CORRECTING DEFECT 11 (vertices=2604, convex hull=886) After retessellation of defect 11, euler #=-16 (146392,438788,292380) : difference with theory (-15) = 1 CORRECTING DEFECT 12 (vertices=5, convex hull=20) After retessellation of defect 12, euler #=-15 (146393,438796,292388) : difference with theory (-14) = 1 CORRECTING DEFECT 13 (vertices=208, convex hull=86) After retessellation of defect 13, euler #=-14 (146416,438906,292476) : difference with theory (-13) = 1 CORRECTING DEFECT 14 (vertices=23, convex hull=64) After retessellation of defect 14, euler #=-13 (146425,438955,292517) : difference with theory (-12) = 1 CORRECTING DEFECT 15 (vertices=7, convex hull=15) After retessellation of defect 15, euler #=-12 (146427,438964,292525) : difference with theory (-11) = 1 CORRECTING DEFECT 16 (vertices=27, convex hull=47) After retessellation of defect 16, euler #=-10 (146428,438986,292548) : difference with theory (-10) = 0 CORRECTING DEFECT 17 (vertices=63, convex hull=73) After retessellation of defect 17, euler #=-9 (146446,439071,292616) : difference with theory (-9) = 0 CORRECTING DEFECT 18 (vertices=91, convex hull=67) After retessellation of defect 18, euler #=-8 (146457,439138,292673) : difference with theory (-8) = 0 CORRECTING DEFECT 19 (vertices=32, convex hull=27) After retessellation of defect 19, euler #=-7 (146463,439162,292692) : difference with theory (-7) = 0 CORRECTING DEFECT 20 (vertices=50, convex hull=91) After retessellation of defect 20, euler #=-6 (146490,439279,292783) : difference with theory (-6) = 0 CORRECTING DEFECT 21 (vertices=9, convex hull=11) After retessellation of defect 21, euler #=-5 (146492,439288,292791) : difference with theory (-5) = 0 CORRECTING DEFECT 22 (vertices=88, convex hull=41) After retessellation of defect 22, euler #=-4 (146501,439331,292826) : difference with theory (-4) = 0 CORRECTING DEFECT 23 (vertices=179, convex hull=30) After retessellation of defect 23, euler #=-3 (146509,439366,292854) : difference with theory (-3) = 0 CORRECTING DEFECT 24 (vertices=5, convex hull=17) After retessellation of defect 24, euler #=-2 (146510,439372,292860) : difference with theory (-2) = 0 CORRECTING DEFECT 25 (vertices=158, convex hull=150) After retessellation of defect 25, euler #=-1 (146530,439500,292969) : difference with theory (-1) = 0 CORRECTING DEFECT 26 (vertices=36, convex hull=73) After retessellation of defect 26, euler #=0 (146549,439589,293040) : difference with theory (0) = 0 CORRECTING DEFECT 27 (vertices=57, convex hull=74) After retessellation of defect 27, euler #=1 (146576,439698,293123) : difference with theory (1) = 0 CORRECTING DEFECT 28 (vertices=21, convex hull=62) After retessellation of defect 28, euler #=2 (146586,439752,293168) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.27 (0.05-->13.09) (max @ vno 105705 --> 151431) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.27 (0.05-->13.09) (max @ vno 105705 --> 151431) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 121 mutations (36.3%), 212 crossovers (63.7%), 763 vertices were eliminated building final representation... 7010 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=146586, nf=293168, ne=439752, g=0) writing corrected surface to /data/MOODS2/freesurfer/1005/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 90.0 minutes 0 defective edges removing intersecting faces 000: 1075 intersecting 001: 285 intersecting 002: 164 intersecting 003: 131 intersecting 004: 108 intersecting 005: 84 intersecting 006: 61 intersecting 007: 38 intersecting 008: 33 intersecting 009: 35 intersecting 010: 31 intersecting 011: 27 intersecting 012: 28 intersecting 013: 32 intersecting 014: 33 intersecting 015: 34 intersecting 016: 33 intersecting 017: 32 intersecting 018: 31 intersecting 019: 29 intersecting 020: 23 intersecting expanding nbhd size to 2 021: 23 intersecting expanding nbhd size to 3 022: 23 intersecting 023: 22 intersecting 024: 17 intersecting 025: 4 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 146586 - 439752 + 293168 = 2 --> 0 holes F =2V-4: 293168 = 293172-4 (0) 2E=3F: 879504 = 879504 (0) total defect index = 0 /data/MOODS2/freesurfer/1005/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.01 hours removing intersecting faces 000: 477 intersecting 001: 262 intersecting 002: 161 intersecting 003: 134 intersecting 004: 106 intersecting 005: 82 intersecting 006: 74 intersecting 007: 44 intersecting 008: 33 intersecting 009: 30 intersecting 010: 39 intersecting 011: 40 intersecting 012: 44 intersecting 013: 31 intersecting 014: 26 intersecting expanding nbhd size to 2 015: 26 intersecting expanding nbhd size to 3 016: 26 intersecting 017: 30 intersecting 018: 19 intersecting 019: 9 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make Final Surf lh Fri Jun 19 22:50:37 CEST 2009 /data/MOODS2/freesurfer/1005/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs 1005 lh not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.99.2.3 2008/01/07 22:30:43 nicks Exp $ $Id: mrisurf.c,v 1.557.2.13 2008/05/23 00:06:05 nicks Exp $ reading volume /data/MOODS2/freesurfer/1005/mri/filled.mgz... reading volume /data/MOODS2/freesurfer/1005/mri/brain.finalsurfs.mgz... reading volume /data/MOODS2/freesurfer/1005/mri/wm.mgz... 19451 bright wm thresholded. 2728 bright non-wm voxels segmented. reading original surface position from /data/MOODS2/freesurfer/1005/surf/lh.orig... computing class statistics... border white: 297304 voxels (1.77%) border gray 317856 voxels (1.89%) WM (103.0): 103.0 +- 5.4 [70.0 --> 110.0] GM (89.0) : 87.1 +- 10.0 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 76.0 (was 70) setting MAX_BORDER_WHITE to 111.4 (was 105) setting MIN_BORDER_WHITE to 86.0 (was 85) setting MAX_CSF to 66.0 (was 40) setting MAX_GRAY to 100.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 81.0 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 56.0 (was 40) repositioning cortical surface to gray/white boundary smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.23 (0.02-->6.60) (max @ vno 145769 --> 145797) face area 0.28 +- 0.13 (0.00-->5.42) CTABfindName: ct was NULL smoothing contralateral hemisphere... intensity peaks found at WM=106, GM=86 using class modes intead of means.... mean inside = 100.2, mean outside = 90.2 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean absolute distance = 0.84 +- 1.11 4239 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... mean border=93.5, 489 (489) missing vertices, mean dist 0.2 [0.8 (%37.4)->0.8 (%62.6))] %65 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=impsy, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.25 (0.04-->6.46) (max @ vno 145769 --> 145797) face area 0.28 +- 0.13 (0.00-->5.03) vertex spacing 0.91 +- 0.27 (0.03-->6.38) (max @ vno 145769 --> 145797) face area 0.28 +- 0.14 (0.00-->4.68) smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.07-->6.37) (max @ vno 145769 --> 145797) face area 0.28 +- 0.14 (0.00-->4.80) CTABfindName: ct was NULL 000: dt: 0.0000, sse=3771411.5, rms=6.61 001: dt: 0.5000, sse=4450930.0, rms=5.03 002: dt: 0.5000, sse=4416178.5, rms=4.04 003: dt: 0.5000, sse=4412214.0, rms=3.47 004: dt: 0.5000, sse=4312847.0, rms=3.09 005: dt: 0.5000, sse=4236032.0, rms=2.81 006: dt: 0.5000, sse=4159073.5, rms=2.63 007: dt: 0.5000, sse=4134121.2, rms=2.50 008: dt: 0.5000, sse=4114773.0, rms=2.38 009: dt: 0.5000, sse=4104937.5, rms=2.27 rms = 2.23, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=4089229.8, rms=2.23 011: dt: 0.2500, sse=3270173.0, rms=2.04 rms = 2.00, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3198994.2, rms=2.00 rms = 1.99, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3186175.5, rms=1.99 positioning took 15.6 minutes inhibiting deformation at non-cortical midline structures... mean absolute distance = 0.51 +- 0.87 4704 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... removing 3 vertex label from ripped group mean border=94.8, 454 (224) missing vertices, mean dist -0.3 [0.6 (%62.0)->0.3 (%38.0))] %71 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=impsy, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.90 +- 0.26 (0.02-->6.33) (max @ vno 145769 --> 145797) face area 0.34 +- 0.17 (0.00-->6.10) vertex spacing 0.90 +- 0.26 (0.05-->6.41) (max @ vno 60040 --> 145586) face area 0.34 +- 0.17 (0.00-->6.40) smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.26 (0.02-->6.49) (max @ vno 60040 --> 145586) face area 0.34 +- 0.17 (0.00-->6.55) CTABfindName: ct was NULL 000: dt: 0.0000, sse=3511096.0, rms=3.29 014: dt: 0.5000, sse=3734400.8, rms=2.47 015: dt: 0.5000, sse=3872018.2, rms=2.20 016: dt: 0.5000, sse=3848577.0, rms=2.07 017: dt: 0.5000, sse=3925632.5, rms=1.96 018: dt: 0.5000, sse=3892586.8, rms=1.89 019: dt: 0.5000, sse=4011483.2, rms=1.84 rms = 1.81, time step reduction 1 of 3 to 0.250... 020: dt: 0.5000, sse=3968989.8, rms=1.81 021: dt: 0.2500, sse=3536467.0, rms=1.69 rms = 1.66, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3461728.8, rms=1.66 rms = 1.63, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3449749.0, rms=1.63 positioning took 7.9 minutes inhibiting deformation at non-cortical midline structures... mean absolute distance = 0.46 +- 0.63 5707 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... mean border=96.5, 504 (154) missing vertices, mean dist -0.3 [0.5 (%68.4)->0.3 (%31.6))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=impsy, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 vertex spacing 0.88 +- 0.26 (0.05-->6.61) (max @ vno 60040 --> 145586) face area 0.33 +- 0.17 (0.00-->6.74) vertex spacing 0.88 +- 0.26 (0.05-->6.58) (max @ vno 60040 --> 145586) face area 0.33 +- 0.17 (0.00-->6.56) smoothing T1 volume with sigma = 0.250 vertex spacing 0.88 +- 0.26 (0.05-->6.58) (max @ vno 60040 --> 145586) face area 0.33 +- 0.17 (0.00-->6.56) CTABfindName: ct was NULL 000: dt: 0.0000, sse=3592205.5, rms=2.93 024: dt: 0.5000, sse=3784715.5, rms=2.03 025: dt: 0.5000, sse=3926720.8, rms=1.75 026: dt: 0.5000, sse=3877864.2, rms=1.70 027: dt: 0.5000, sse=3974803.5, rms=1.61 rms = 1.63, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3731222.5, rms=1.55 rms = 1.51, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3609876.2, rms=1.51 rms = 1.51, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3595350.0, rms=1.51 positioning took 5.8 minutes inhibiting deformation at non-cortical midline structures... mean absolute distance = 0.36 +- 0.48 4796 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... mean border=97.3, 549 (131) missing vertices, mean dist -0.1 [0.4 (%59.9)->0.3 (%40.1))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=impsy, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 CTABfindName: ct was NULL 000: dt: 0.0000, sse=3608966.5, rms=1.91 031: dt: 0.5000, sse=4149998.5, rms=1.49 rms = 1.50, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3979092.5, rms=1.42 rms = 1.43, time step reduction 2 of 3 to 0.125... rms = 1.41, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3952440.0, rms=1.41 positioning took 2.8 minutes inhibiting deformation at non-cortical midline structures... writing white matter surface to /data/MOODS2/freesurfer/1005/surf/lh.white... writing smoothed curvature to lh.curv correcting aseg with surfaces... label Left_Hippocampus: removing 15 voxels in segment 0 label Left_Hippocampus: removing 1261 voxels in segment 1 label Left_Hippocampus: removing 10 voxels in segment 2 label Left_Hippocampus: removing 144 voxels in segment 3 label Left_Hippocampus: removing 9 voxels in segment 4 label Left_Hippocampus: removing 1 voxels in segment 5 label Left_Hippocampus: removing 18 voxels in segment 6 label Left_Hippocampus: removing 4 voxels in segment 7 label Left_Hippocampus: removing 6915 voxels in segment 9 label Left_Hippocampus: removing 98 voxels in segment 10 label Left_Hippocampus: removing 11 voxels in segment 11 label Left_Hippocampus: removing 204 voxels in segment 12 generating cortex label... 9 non-cortical segments detected only using segment with 2501 vertices erasing segment 1 (vno[0] = 95775) erasing segment 2 (vno[0] = 98314) erasing segment 3 (vno[0] = 103350) erasing segment 4 (vno[0] = 106397) erasing segment 5 (vno[0] = 107481) erasing segment 6 (vno[0] = 111225) erasing segment 7 (vno[0] = 112815) erasing segment 8 (vno[0] = 115526) writing cortex label to /data/MOODS2/freesurfer/1005/label/lh.cortex.label... LabelWrite: saving to /data/MOODS2/freesurfer/1005/label/lh.cortex.label writing curvature file /data/MOODS2/freesurfer/1005/surf/lh.curv writing smoothed area to lh.area writing curvature file /data/MOODS2/freesurfer/1005/surf/lh.area vertex spacing 0.87 +- 0.26 (0.05-->6.60) (max @ vno 60040 --> 145586) face area 0.32 +- 0.17 (0.00-->6.39) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=76.6, 309 (309) missing vertices, mean dist 1.7 [2.0 (%0.2)->3.0 (%99.8))] %23 local maxima, %31 large gradients and %42 min vals, 2287 gradients ignored tol=1.0e-04, sigma=2.0, host=impsy, 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 0.85 +- 0.28 (0.02-->6.59) (max @ vno 60040 --> 145586) face area 0.28 +- 0.17 (0.00-->4.71) vertex spacing 0.92 +- 0.35 (0.03-->6.63) (max @ vno 60040 --> 145586) face area 0.28 +- 0.19 (0.00-->5.69) vertex spacing 0.96 +- 0.39 (0.02-->6.70) (max @ vno 60040 --> 145586) face area 0.28 +- 0.20 (0.00-->5.78) vertex spacing 0.97 +- 0.40 (0.01-->6.66) (max @ vno 60040 --> 145586) face area 0.28 +- 0.21 (0.00-->5.86) vertex spacing 0.96 +- 0.41 (0.05-->6.66) (max @ vno 60040 --> 145586) face area 0.28 +- 0.22 (0.00-->5.86) smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=15678263.0, rms=21.65 001: dt: 0.5000, sse=13347292.0, rms=19.64 002: dt: 0.5000, sse=11409069.0, rms=17.84 003: dt: 0.5000, sse=9827236.0, rms=16.21 004: dt: 0.5000, sse=8575858.0, rms=14.72 005: dt: 0.5000, sse=7639342.5, rms=13.36 006: dt: 0.5000, sse=6917319.0, rms=12.09 007: dt: 0.5000, sse=6407417.0, rms=10.88 008: dt: 0.5000, sse=6040792.0, rms=9.74 009: dt: 0.5000, sse=5813944.0, rms=8.63 010: dt: 0.5000, sse=5643142.0, rms=7.57 011: dt: 0.5000, sse=5510681.5, rms=6.61 012: dt: 0.5000, sse=5514327.5, rms=5.79 013: dt: 0.5000, sse=5556859.5, rms=5.15 014: dt: 0.5000, sse=5659623.0, rms=4.70 015: dt: 0.5000, sse=5686771.5, rms=4.37 016: dt: 0.5000, sse=5759414.5, rms=4.14 017: dt: 0.5000, sse=5770490.5, rms=3.97 018: dt: 0.5000, sse=5818643.0, rms=3.82 019: dt: 0.5000, sse=5843590.5, rms=3.74 020: dt: 0.5000, sse=5832267.0, rms=3.65 rms = 3.60, time step reduction 1 of 3 to 0.250... 021: dt: 0.5000, sse=5854762.0, rms=3.60 022: dt: 0.2500, sse=4085450.2, rms=3.06 023: dt: 0.2500, sse=3911492.8, rms=2.94 rms = 2.94, time step reduction 2 of 3 to 0.125... 024: dt: 0.2500, sse=3857674.5, rms=2.94 025: dt: 0.1250, sse=3656499.5, rms=2.80 rms = 2.77, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3620136.5, rms=2.77 positioning took 30.6 minutes mean border=75.5, 2222 (79) missing vertices, mean dist 0.2 [0.2 (%43.2)->0.6 (%56.8))] %38 local maxima, %22 large gradients and %35 min vals, 1455 gradients ignored tol=1.0e-04, sigma=1.0, host=impsy, 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 vertex spacing 0.97 +- 0.41 (0.04-->6.89) (max @ vno 95777 --> 94614) face area 0.37 +- 0.28 (0.00-->7.62) smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4024502.8, rms=3.85 027: dt: 0.5000, sse=4424155.5, rms=3.61 028: dt: 0.5000, sse=5202943.5, rms=3.46 rms = 3.54, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=4477280.0, rms=3.04 030: dt: 0.2500, sse=4192388.8, rms=2.91 rms = 2.93, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=4129038.8, rms=2.86 032: dt: 0.1250, sse=4017766.0, rms=2.79 rms = 2.77, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3984854.8, rms=2.77 positioning took 6.5 minutes mean border=75.0, 2799 (61) missing vertices, mean dist 0.1 [0.2 (%43.7)->0.4 (%56.3))] %47 local maxima, %13 large gradients and %34 min vals, 1445 gradients ignored tol=1.0e-04, sigma=0.5, host=impsy, 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 0.96 +- 0.41 (0.04-->7.00) (max @ vno 95777 --> 94614) face area 0.37 +- 0.29 (0.00-->7.70) smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4028519.5, rms=3.00 rms = 3.23, time step reduction 1 of 3 to 0.250... 034: dt: 0.2500, sse=3945394.5, rms=2.82 rms = 2.78, time step reduction 2 of 3 to 0.125... 035: dt: 0.2500, sse=4013500.0, rms=2.78 036: dt: 0.1250, sse=3937864.2, rms=2.71 rms = 2.68, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3971651.8, rms=2.68 positioning took 3.7 minutes mean border=74.6, 5541 (53) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.3 (%53.4))] %49 local maxima, %10 large gradients and %33 min vals, 1413 gradients ignored tol=1.0e-04, sigma=0.2, host=impsy, 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 0.96 +- 0.41 (0.06-->7.06) (max @ vno 95777 --> 94614) face area 0.37 +- 0.29 (0.00-->7.78) writing pial surface to /data/MOODS2/freesurfer/1005/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3982381.0, rms=2.76 rms = 2.99, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=3957946.8, rms=2.65 rms = 2.61, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=4133635.0, rms=2.61 040: dt: 0.1250, sse=4050692.8, rms=2.54 rms = 2.50, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=4081711.2, rms=2.50 positioning took 3.6 minutes writing curvature file /data/MOODS2/freesurfer/1005/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /data/MOODS2/freesurfer/1005/surf/lh.area.pial vertex spacing 0.96 +- 0.41 (0.06-->7.08) (max @ vno 93484 --> 93465) face area 0.37 +- 0.29 (0.00-->7.79) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 146586 vertices processed 25000 of 146586 vertices processed 50000 of 146586 vertices processed 75000 of 146586 vertices processed 100000 of 146586 vertices processed 125000 of 146586 vertices processed 0 of 146586 vertices processed 25000 of 146586 vertices processed 50000 of 146586 vertices processed 75000 of 146586 vertices processed 100000 of 146586 vertices processed 125000 of 146586 vertices processed thickness calculation complete, 2280:2861 truncations. 57896 vertices at 0 distance 87641 vertices at 1 distance 72122 vertices at 2 distance 35947 vertices at 3 distance 16065 vertices at 4 distance 6732 vertices at 5 distance 2779 vertices at 6 distance 1159 vertices at 7 distance 551 vertices at 8 distance 315 vertices at 9 distance 192 vertices at 10 distance 134 vertices at 11 distance 122 vertices at 12 distance 88 vertices at 13 distance 59 vertices at 14 distance 54 vertices at 15 distance 36 vertices at 16 distance 19 vertices at 17 distance 29 vertices at 18 distance 15 vertices at 19 distance 35 vertices at 20 distance writing curvature file /data/MOODS2/freesurfer/1005/surf/lh.thickness positioning took 87.3 minutes #-------------------------------------------- #@# Surf Volume lh Sat Jun 20 00:17:58 CEST 2009 /data/MOODS2/freesurfer/1005/surf mris_calc -o lh.area.mid lh.area add lh.area.pial mris_calc -o lh.area.mid lh.area.mid div 2 mris_calc -o lh.volume lh.area.mid mul lh.thickness mris_calc: curvature file 'lh.area.mid' has wrong magic number. Linux impsy-pc4 2.6.27.19-3.2-default #1 SMP 2009-02-25 15:40:44 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sat Jun 20 00:17:58 CEST 2009