Fri Feb 2 11:03:55 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer//bin//recon-all -subjid P44W_10588_L1 -autorecon1 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/ Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:55-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:03:56-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Feb 2 11:03:56 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Fri Feb 2 11:04:15 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Fri Feb 2 11:04:18 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Fri Feb 2 11:04:21 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Fri Feb 2 11:04:24 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-2.img Fri Feb 2 11:04:27 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 11:04:27 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-7994/resampled.fslmat flirt: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory ERROR: running flirt Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 2 11:04:27 CST 2007 New invocation of recon-all Fri Feb 2 11:13:47 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer//bin//recon-all -subjid P44W_10588_L1 -autorecon1 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/ Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:13:47-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Feb 2 11:13:47 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Fri Feb 2 11:14:06 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Fri Feb 2 11:14:09 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Fri Feb 2 11:14:12 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Fri Feb 2 11:14:15 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-2.img Fri Feb 2 11:14:18 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 11:14:18 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8533/resampled.fslmat flirt: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory ERROR: running flirt Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 2 11:14:18 CST 2007 New invocation of recon-all Fri Feb 2 11:15:16 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer//bin//recon-all -s P44W_10588_L1 -all subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/ Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-17:15:16-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Feb 2 11:15:16 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Fri Feb 2 11:15:35 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Fri Feb 2 11:15:37 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Fri Feb 2 11:15:40 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Fri Feb 2 11:15:43 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-2.img Fri Feb 2 11:15:46 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 11:15:46 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-8864/resampled.fslmat flirt: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory ERROR: running flirt Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 2 11:15:47 CST 2007 New invocation of recon-all Fri Feb 2 14:33:07 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer/bin//recon-all -subjid P44W_10588_L1 -autorecon1 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:07-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:08-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:33:09-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /usr/local/freesurfer/ #-------------------------------------------- #@# MotionCor Fri Feb 2 14:33:10 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Fri Feb 2 14:33:30 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Fri Feb 2 14:33:33 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Fri Feb 2 14:33:36 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Fri Feb 2 14:33:39 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-2.img Fri Feb 2 14:33:42 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 14:33:42 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-5411/resampled.fslmat flirt: error while loading shared libraries: libstdc++-libc6.2-2.so.3: cannot open shared object file: No such file or directory ERROR: running flirt Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 2 14:33:42 CST 2007 New invocation of recon-all Fri Feb 2 14:53:37 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer/bin//recon-all -subjid P44W_10588_L1 -autorecon1 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-20:53:37-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /usr/local/freesurfer/ #-------------------------------------------- #@# MotionCor Fri Feb 2 14:53:38 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Fri Feb 2 14:53:57 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Fri Feb 2 14:54:01 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Fri Feb 2 14:54:04 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Fri Feb 2 14:54:07 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img Fri Feb 2 14:54:10 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 14:54:10 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Fri Feb 2 14:54:10 CST 2007 Ended at Fri Feb 2 14:59:03 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img Fri Feb 2 14:59:03 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 14:59:03 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Fri Feb 2 14:59:03 CST 2007 Ended at Fri Feb 2 15:03:55 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img Fri Feb 2 15:03:55 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Fri Feb 2 15:03:55 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Fri Feb 2 15:03:55 CST 2007 Ended at Fri Feb 2 15:08:38 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img ----------------------------------------- Averaging Fri Feb 2 15:08:38 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 inhibiting isotropic volume interpolation 1 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-1.img... 2 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-2.img... 3 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-3.img... 4 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/cor-4.img... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/avgvol.img... alignment and averaging took 0 minutes and 39 seconds. Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting Average to output Fri Feb 2 15:09:17 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/avgvol.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -tr 1900 -te 3.93 -TI 1100 -flip_angle 0.261799 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/avgvol.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -tr 1900 -te 3.93 -TI 1100 -flip_angle 0.261799 reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6333/avgvol.img... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz... ----------------------------------------- Started at: Fri Feb 2 14:53:42 CST 2007 Ended at: Fri Feb 2 15:09:26 CST 2007 mri_motion_correct.fsl: done /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) Original Data has (1, 1, 1.25) mm size and (224, 256, 160) 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 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Feb 2 15:09:50 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/P44W_10588_L1/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 1.3.2.1 2006/11/24 20:16:38 nicks Exp $ Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux Fri Feb 2 15:09:50 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.7138 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7138/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7138/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) writing to ./tmp.mri_nu_correct.mni.7138/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Feb 2 15:09:59 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7138/nu0.mnc ./tmp.mri_nu_correct.mni.7138/nu1.mnc [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-02 15:09:59] 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 /var/tmp/nu_correct_7189/ ./tmp.mri_nu_correct.mni.7138/nu0.mnc ./tmp.mri_nu_correct.mni.7138/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() Number of iterations: 43 CV of field change: 0.000984685 [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-02 15:11:15] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7138/nu0.mnc /var/tmp/nu_correct_7189//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 Feb 2 15:11:25 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7138/nu1.mnc ./tmp.mri_nu_correct.mni.7138/nu2.mnc [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-02 15:11:25] 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 /var/tmp/nu_correct_7790/ ./tmp.mri_nu_correct.mni.7138/nu1.mnc ./tmp.mri_nu_correct.mni.7138/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 40 CV of field change: 0.000989415 [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-02 15:12:38] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7138/nu1.mnc /var/tmp/nu_correct_7790//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.7138/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.7138/nu2.mnc nu.mgz --like orig.mgz Can't find the talairach xform '/usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from ./tmp.mri_nu_correct.mni.7138/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) INFO: transform src into the like-volume: orig.mgz Talairach transform /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm writing to nu.mgz... Fri Feb 2 15:13:08 CST 2007 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Fri Feb 2 15:13:08 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/P44W_10588_L1/mri /usr/local/freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux Fri Feb 2 15:13:08 CST 2007 tmpdir is transforms/tmp.talairach.8399 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_convert nu.mgz transforms/tmp.talairach.8399/src.mnc mri_convert nu.mgz transforms/tmp.talairach.8399/src.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from nu.mgz... Talairach transform /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) writing to transforms/tmp.talairach.8399/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.8399/src.mnc transforms/talairach.auto.xfm Fri Feb 2 15:14:08 CST 2007 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Intensity Normalization Fri Feb 2 15:14:09 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.103 0.046 -0.012 -0.075; -0.041 1.039 0.164 -19.026; 0.019 -0.172 1.099 23.452; 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 6 minutes and 3 seconds. white matter peak found at 110 gm peak at 83 (83), valley at 49 (49) csf peak at 34, setting threshold to 66 white matter peak found at 110 gm peak at 83 (83), valley at 42 (42) csf peak at 42, setting threshold to 69 #-------------------------------------------- #@# Skull Stripping Fri Feb 2 15:20:16 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_watershed T1.mgz brainmask.auto.mgz ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 247966 Find the largest 110-component... heap usage = 246736 Kbytes. current max segment has 218351 voxels removing small segments (less than 1 percent of maxarea). heap usage = 104416 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 218351 voxels first estimation of the COG coord: x=128 y=111 z=111 r=88 first estimation of the main basin volume: 2877798 voxels global maximum in x=157, y=109, z=69, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 done Analyze main basin size= 1750515 voxels, voxel volume =1.000 = 1750515 mmm3 = 1750.515 cm3 done PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=109, z=108, r=9753 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=58, TRANSITION=62, GM_MIN=66, GM=84 after analyzing : CSF_MAX=58, TRANSITION=64, GM_MIN=66, GM=69 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* No Rigid alignment: Atlas Mode Off before rotation: sse = 2.05, sigma = 3.74 after rotation: sse = 2.05, sigma = 3.74 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.08, its var is 2.96 before Erosion-Dilatation 0.88% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1698687 voxels, voxel volume = 1.000 mm3 = 1698687 mmm3 = 1698.687 cm3 ****************************** Save...done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ recon-all finished without error at Fri Feb 2 15:22:16 CST 2007 New invocation of recon-all Fri Feb 2 16:15:28 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer//bin//recon-all -subjid P44W_10588_L1 -autorecon2 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer/ Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/02-22:15:28-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### #------------------------------------- #@# EM Registration Fri Feb 2 16:15:28 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer//average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-2.8, 9.7, -5.1): log p = -15685.1 Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-15685.1 (thresh=-15669.4) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-12180.5 (thresh=-12168.3) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... fp = 12131.479492, fret = 12131.479492, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... pass 5 through quasi-newton minimization... pass 6 through quasi-newton minimization... freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 initial log_p = -31639.6 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 002: -log(p) = 12180.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 003: -log(p) = 12176.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 004: -log(p) = 12144.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 005: -log(p) = 12131.5 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) outof QuasiNewtonEMA: 007: -log(p) = 12131.5 tol 0.000010 Resulting transform: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -12180.5 (old=-31639.6) transform before final EM align: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 006: -log(p) = 1488031.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 007: -log(p) = 1474529.9 after pass:transform: ( 1.06, 0.00, 0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.01, -0.13, 1.00, 11.11) dfp_em_step_func: 008: -log(p) = 1463433.4 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 009: -log(p) = 1456579.2 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 010: -log(p) = 1455069.6 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 011: -log(p) = 1454569.5 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) outof QuasiNewtonEMA: 013: -log(p) = 1454455.0 tol 0.000000 final transform: 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 7 minutes and 32 seconds. #-------------------------------------- #@# CA Normalize Fri Feb 2 16:23:00 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer//average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (128, 48, 31) --> (191, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 118.0 688 of 3149 (21.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (68, 48, 31) --> (128, 153, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 119.0 413 of 3134 (13.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (130, 131, 57) --> (174, 170, 111) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 112.0 70 of 199 (35.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (85, 133, 55) --> (128, 170, 111) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 110.0 59 of 188 (31.4%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (111, 118, 92) --> (143, 185, 122) Brain_Stem: limiting intensities to 95.0 --> 106.0 106 of 264 (40.2%) samples deleted using 6934 total control points for intensity normalization... bias field = 1.016 +- 0.060 24 of 5598 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 34 seconds. #-------------------------------------- #@# CA Reg Fri Feb 2 16:24:34 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer//average/RB_all_2006-02-15.gca transforms/talairach.m3z renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 not handling expanded ventricles... using MR volume brainmask.mgz to mask input volume... using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer//average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) renormalizing by structure alignment.... renormalizing input #0 aligning Left_Pallidum... gca peak = 0.11705 (100) mri peak = 0.15616 (105) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (650 voxels, overlap=0.725) aligning Right_Pallidum... gca peak = 0.13501 (106) mri peak = 0.14880 (104) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (996 voxels, overlap=0.633) aligning Right_Cerebral_White_Matter... gca peak = 0.05652 (116) mri peak = 0.07673 (115) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (109779 voxels, overlap=0.532) aligning Left_Cerebral_White_Matter... gca peak = 0.05682 (116) mri peak = 0.05484 (115) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (129515 voxels, overlap=0.428) aligning Left_Lateral_Ventricle... gca peak = 0.05153 (25) mri peak = 0.04526 (33) Left_Lateral_Ventricle (4): linear fit = 1.55 x + 0.0 (5475 voxels, overlap=0.181) aligning Right_Lateral_Ventricle... gca peak = 0.07557 (30) mri peak = 0.06721 (31) Right_Lateral_Ventricle (43): linear fit = 1.30 x + 0.0 (5308 voxels, overlap=0.203) aligning Right_Hippocampus... gca peak = 0.14805 (66) mri peak = 0.10387 (80) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (2085 voxels, overlap=0.058) aligning Left_Hippocampus... gca peak = 0.17297 (66) mri peak = 0.09064 (81) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1694 voxels, overlap=0.057) aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.02939 (84) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.03178 (81) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (142002 voxels, overlap=0.108) aligning Right_Caudate... gca peak = 0.07786 (81) mri peak = 0.14952 (93) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1616 voxels, overlap=0.125) aligning Left_Caudate... gca peak = 0.07814 (81) mri peak = 0.11678 (90) Killed ERROR: mri_ca_register with non-zero status Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 2 17:29:36 CST 2007 New invocation of recon-all Mon Feb 5 16:44:57 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer/bin//recon-all -subjid P44W_10588_L1 -autorecon2 subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:58-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/05-22:44:59-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /usr/local/freesurfer/ #------------------------------------- #@# EM Registration Mon Feb 5 16:45:00 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-2.8, 9.7, -5.1): log p = -15685.1 Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-15685.1 (thresh=-15669.4) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-12180.5 (thresh=-12168.3) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... fp = 12131.479492, fret = 12131.479492, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... pass 5 through quasi-newton minimization... pass 6 through quasi-newton minimization... freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 initial log_p = -31639.6 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 002: -log(p) = 12180.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 003: -log(p) = 12176.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 004: -log(p) = 12144.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 005: -log(p) = 12131.5 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) outof QuasiNewtonEMA: 007: -log(p) = 12131.5 tol 0.000010 Resulting transform: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -12180.5 (old=-31639.6) transform before final EM align: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 006: -log(p) = 1488031.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 007: -log(p) = 1474529.9 after pass:transform: ( 1.06, 0.00, 0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.01, -0.13, 1.00, 11.11) dfp_em_step_func: 008: -log(p) = 1463433.4 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 009: -log(p) = 1456579.2 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 010: -log(p) = 1455069.6 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 011: -log(p) = 1454569.5 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) outof QuasiNewtonEMA: 013: -log(p) = 1454455.0 tol 0.000000 final transform: 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 6 minutes and 7 seconds. #-------------------------------------- #@# CA Normalize Mon Feb 5 16:51:07 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (128, 48, 31) --> (191, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 118.0 688 of 3149 (21.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (68, 48, 31) --> (128, 153, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 119.0 413 of 3134 (13.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (130, 131, 57) --> (174, 170, 111) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 112.0 70 of 199 (35.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (85, 133, 55) --> (128, 170, 111) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 110.0 59 of 188 (31.4%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (111, 118, 92) --> (143, 185, 122) Brain_Stem: limiting intensities to 95.0 --> 106.0 106 of 264 (40.2%) samples deleted using 6934 total control points for intensity normalization... bias field = 1.016 +- 0.060 24 of 5598 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 19 seconds. #-------------------------------------- #@# CA Reg Mon Feb 5 16:52:27 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.m3z renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 not handling expanded ventricles... using MR volume brainmask.mgz to mask input volume... using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) renormalizing by structure alignment.... renormalizing input #0 aligning Left_Pallidum... gca peak = 0.11705 (100) mri peak = 0.15616 (105) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (650 voxels, overlap=0.725) aligning Right_Pallidum... gca peak = 0.13501 (106) mri peak = 0.14880 (104) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (996 voxels, overlap=0.633) aligning Right_Cerebral_White_Matter... gca peak = 0.05652 (116) mri peak = 0.07673 (115) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (109779 voxels, overlap=0.532) aligning Left_Cerebral_White_Matter... gca peak = 0.05682 (116) mri peak = 0.05484 (115) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (129515 voxels, overlap=0.428) aligning Left_Lateral_Ventricle... gca peak = 0.05153 (25) mri peak = 0.04526 (33) Left_Lateral_Ventricle (4): linear fit = 1.55 x + 0.0 (5475 voxels, overlap=0.181) aligning Right_Lateral_Ventricle... gca peak = 0.07557 (30) mri peak = 0.06721 (31) Right_Lateral_Ventricle (43): linear fit = 1.30 x + 0.0 (5308 voxels, overlap=0.203) aligning Right_Hippocampus... gca peak = 0.14805 (66) mri peak = 0.10387 (80) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (2085 voxels, overlap=0.058) aligning Left_Hippocampus... gca peak = 0.17297 (66) mri peak = 0.09064 (81) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1694 voxels, overlap=0.057) aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.02939 (84) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.03178 (81) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (142002 voxels, overlap=0.108) aligning Right_Caudate... gca peak = 0.07786 (81) mri peak = 0.14952 (93) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1616 voxels, overlap=0.125) aligning Left_Caudate... gca peak = 0.07814 (81) mri peak = 0.11678 (90) Left_Caudate (11): linear fit = 1.10 x + 0.0 (1408 voxels, overlap=0.372) aligning Left_Cerebellum_Cortex... gca peak = 0.06033 (63) mri peak = 0.06077 (86) overlap = 0.000534633, overlap_threshold = 0.001 insufficient overlap 0.0005 in histograms - rejecting aligning Right_Cerebellum_Cortex... gca peak = 0.05990 (64) mri peak = 0.06449 (83) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (35986 voxels, overlap=0.008) aligning Left_Cerebellum_White_Matter... gca peak = 0.09299 (92) mri peak = 0.06522 (103) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (16273 voxels, overlap=0.585) aligning Right_Cerebellum_White_Matter... gca peak = 0.08899 (93) mri peak = 0.07489 (101) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (13032 voxels, overlap=0.731) aligning Left_Amygdala... gca peak = 0.13911 (71) mri peak = 0.13070 (79) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (911 voxels, overlap=0.047) aligning Right_Amygdala... gca peak = 0.15703 (65) mri peak = 0.11577 (80) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (973 voxels, overlap=0.012) aligning Left_Thalamus_Proper... gca peak = 0.06537 (100) mri peak = 0.09795 (103) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3335 voxels, overlap=0.520) aligning Right_Thalamus_Proper... gca peak = 0.07019 (99) mri peak = 0.11165 (102) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3212 voxels, overlap=0.501) aligning Left_Putamen... gca peak = 0.09468 (90) mri peak = 0.13402 (94) Left_Putamen (12): linear fit = 1.08 x + 0.0 (3118 voxels, overlap=0.440) aligning Right_Putamen... gca peak = 0.07184 (82) mri peak = 0.11033 (94) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2899 voxels, overlap=0.476) aligning Brain_Stem... gca peak = 0.05597 (80) mri peak = 0.11599 (98) Brain_Stem (16): linear fit = 1.02 x + 0.0 (13631 voxels, overlap=0.309) aligning Right_VentralDC... gca peak = 0.05879 (97) mri peak = 0.08127 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2695 voxels, overlap=0.476) aligning Left_VentralDC... gca peak = 0.06932 (98) mri peak = 0.07580 (105) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2707 voxels, overlap=0.524) aligning Third_Ventricle... gca peak = 0.10105 (38) mri peak = 0.06389 (32) Third_Ventricle (14): linear fit = 0.93 x + 0.0 (410 voxels, overlap=0.394) aligning Fourth_Ventricle... gca peak = 0.10426 (32) mri peak = 0.12812 (31) not using caudate to estimate GM means setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 1.23 x + 0 setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.33 x + 0 Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (1020 voxels, overlap=0.399) estimating mean gm scale to be 1.20 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.18 x + 0.0 24 transforms computed 0000: dt=0.000000, rms=0.735 (1.447%), neg=0, invalid=1511, LIN 0001: dt=0.000000, rms=0.728 (0.866%), neg=0, invalid=1511, LIN 0002: dt=0.000000, rms=0.726 (0.358%), neg=0, invalid=1511, LIN rms increased - undoing step... 0003: dt=0.000000, rms=0.725 (-0.005%), neg=0, invalid=1511, LIN rms increased - undoing step... 0005: dt=0.000000, rms=0.725 (-0.063%), neg=0, invalid=1511, LIN rms increased - undoing step... 0007: dt=0.000000, rms=0.724 (-0.241%), neg=0, invalid=1511, LIN rms increased - undoing step... 0009: dt=0.000000, rms=0.724 (-0.241%), neg=0, invalid=1511, LIN rms increased - undoing step... 0011: dt=0.000000, rms=0.723 (-0.267%), neg=0, invalid=1511, LIN rms increased - undoing step... 0013: dt=0.000000, rms=0.723 (-0.271%), neg=0, invalid=1511, LIN rms increased - undoing step... 0015: dt=0.000000, rms=0.723 (-0.280%), neg=0, invalid=1511, LIN rms increased - undoing step... 0017: dt=0.000000, rms=0.723 (-0.279%), neg=0, invalid=1511, LIN label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.720, neg=0, invalid=1511 0020: dt=216.726087, rms=0.671 (6.795%), neg=0, invalid=1511 0021: dt=153.403277, rms=0.653 (2.584%), neg=0, invalid=1511 0022: dt=199.377710, rms=0.645 (1.304%), neg=0, invalid=1511 0023: dt=141.398197, rms=0.640 (0.795%), neg=0, invalid=1511 0024: dt=221.952003, rms=0.635 (0.774%), neg=0, invalid=1511 0025: dt=120.120189, rms=0.632 (0.380%), neg=0, invalid=1511 0026: dt=517.888008, rms=0.627 (0.808%), neg=0, invalid=1511 0027: dt=87.443621, rms=0.624 (0.473%), neg=0, invalid=1511 0028: dt=2071.552031, rms=0.616 (1.395%), neg=0, invalid=1511 0029: dt=116.849928, rms=0.612 (0.587%), neg=0, invalid=1511 0030: dt=129.472002, rms=0.611 (0.105%), neg=0, invalid=1511 0031: dt=517.888008, rms=0.610 (0.185%), neg=0, invalid=1511 0032: dt=85.507087, rms=0.609 (0.138%), neg=0, invalid=1511 0033: dt=2071.552031, rms=0.605 (0.647%), neg=0, invalid=1511 0034: dt=92.480001, rms=0.605 (0.077%), neg=0, invalid=1511 0035: dt=517.888008, rms=0.604 (0.166%), neg=0, invalid=1511 0036: dt=129.472002, rms=0.604 (0.045%), neg=0, invalid=1511 0037: dt=129.472002, rms=0.603 (0.036%), neg=0, invalid=1511 0038: dt=129.472002, rms=0.603 (0.061%), neg=0, invalid=1511 0039: dt=129.472002, rms=0.603 (0.080%), neg=0, invalid=1511 0040: dt=129.472002, rms=0.602 (0.099%), neg=0, invalid=1511 0041: dt=129.472002, rms=0.601 (0.122%), neg=0, invalid=1511 0042: dt=129.472002, rms=0.600 (0.122%), neg=0, invalid=1511 0043: dt=129.472002, rms=0.600 (0.145%), neg=0, invalid=1511 0044: dt=129.472002, rms=0.599 (0.138%), neg=0, invalid=1511 0045: dt=129.472002, rms=0.598 (0.119%), neg=0, invalid=1511 0046: dt=129.472002, rms=0.597 (0.105%), neg=0, invalid=1511 0047: dt=129.472002, rms=0.597 (0.134%), neg=0, invalid=1511 0048: dt=129.472002, rms=0.596 (0.141%), neg=0, invalid=1511 0049: dt=129.472002, rms=0.595 (0.143%), neg=0, invalid=1511 0050: dt=129.472002, rms=0.594 (0.125%), neg=0, invalid=1511 0051: dt=129.472002, rms=0.594 (0.104%), neg=0, invalid=1511 0052: dt=129.472002, rms=0.593 (0.098%), neg=0, invalid=1511 0053: dt=129.472002, rms=0.592 (0.124%), neg=0, invalid=1511 0054: dt=129.472002, rms=0.592 (0.115%), neg=0, invalid=1511 0055: dt=129.472002, rms=0.591 (0.071%), neg=0, invalid=1511 0056: dt=129.472002, rms=0.591 (0.070%), neg=0, invalid=1511 0057: dt=129.472002, rms=0.590 (0.080%), neg=0, invalid=1511 0058: dt=129.472002, rms=0.590 (0.111%), neg=0, invalid=1511 0059: dt=129.472002, rms=0.589 (0.092%), neg=0, invalid=1511 0060: dt=129.472002, rms=0.589 (0.051%), neg=0, invalid=1511 0061: dt=129.472002, rms=0.588 (0.061%), neg=0, invalid=1511 0062: dt=129.472002, rms=0.588 (0.131%), neg=0, invalid=1511 0063: dt=129.472002, rms=0.587 (0.100%), neg=0, invalid=1511 0064: dt=129.472002, rms=0.587 (0.049%), neg=0, invalid=1511 0065: dt=129.472002, rms=0.587 (0.026%), neg=0, invalid=1511 0066: dt=129.472002, rms=0.586 (0.058%), neg=0, invalid=1511 0067: dt=129.472002, rms=0.586 (0.093%), neg=0, invalid=1511 0068: dt=129.472002, rms=0.585 (0.081%), neg=0, invalid=1511 0069: dt=129.472002, rms=0.585 (0.058%), neg=0, invalid=1511 0070: dt=129.472002, rms=0.585 (0.043%), neg=0, invalid=1511 0071: dt=129.472002, rms=0.584 (0.044%), neg=0, invalid=1511 0072: dt=129.472002, rms=0.584 (0.056%), neg=0, invalid=1511 0073: dt=129.472002, rms=0.584 (0.044%), neg=0, invalid=1511 0074: dt=129.472002, rms=0.584 (0.042%), neg=0, invalid=1511 0075: dt=129.472002, rms=0.583 (0.072%), neg=0, invalid=1511 0076: dt=129.472002, rms=0.583 (0.044%), neg=0, invalid=1511 0077: dt=129.472002, rms=0.583 (0.025%), neg=0, invalid=1511 0078: dt=129.472002, rms=0.583 (0.017%), neg=0, invalid=1511 0079: dt=129.472002, rms=0.582 (0.057%), neg=0, invalid=1511 0080: dt=129.472002, rms=0.582 (0.066%), neg=0, invalid=1511 0081: dt=129.472002, rms=0.582 (0.041%), neg=0, invalid=1511 0082: dt=129.472002, rms=0.582 (-0.004%), neg=0, invalid=1511 0083: dt=0.000000, rms=0.582 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=1511 0084: dt=369.920006, rms=0.580 (0.218%), neg=0, invalid=1511 0085: dt=73.984001, rms=0.580 (0.006%), neg=0, invalid=1511 0086: dt=73.984001, rms=0.580 (0.013%), neg=0, invalid=1511 0087: dt=73.984001, rms=0.580 (0.011%), neg=0, invalid=1511 0088: dt=73.984001, rms=0.580 (0.019%), neg=0, invalid=1511 0089: dt=73.984001, rms=0.580 (0.028%), neg=0, invalid=1511 0090: dt=73.984001, rms=0.580 (0.048%), neg=0, invalid=1511 0091: dt=73.984001, rms=0.579 (0.047%), neg=0, invalid=1511 0092: dt=73.984001, rms=0.579 (0.038%), neg=0, invalid=1511 0093: dt=73.984001, rms=0.579 (0.029%), neg=0, invalid=1511 0094: dt=73.984001, rms=0.579 (0.032%), neg=0, invalid=1511 0095: dt=73.984001, rms=0.579 (0.040%), neg=0, invalid=1511 0096: dt=73.984001, rms=0.578 (0.028%), neg=0, invalid=1511 0097: dt=73.984001, rms=0.578 (0.020%), neg=0, invalid=1511 0098: dt=73.984001, rms=0.578 (0.022%), neg=0, invalid=1511 0099: dt=73.984001, rms=0.578 (0.039%), neg=0, invalid=1511 0100: dt=73.984001, rms=0.578 (0.038%), neg=0, invalid=1511 0101: dt=73.984001, rms=0.578 (0.026%), neg=0, invalid=1511 0102: dt=73.984001, rms=0.577 (0.026%), neg=0, invalid=1511 0103: dt=73.984001, rms=0.577 (0.023%), neg=0, invalid=1511 0104: dt=73.984001, rms=0.577 (0.018%), neg=0, invalid=1511 0105: dt=517.888008, rms=0.577 (0.039%), neg=0, invalid=1511 0106: dt=0.000000, rms=0.577 (-0.001%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=1511 0107: dt=111.282571, rms=0.577 (0.389%), neg=0, invalid=1511 0108: dt=215.193044, rms=0.569 (1.306%), neg=0, invalid=1511 0109: dt=35.055124, rms=0.568 (0.321%), neg=0, invalid=1511 0110: dt=49.053035, rms=0.567 (0.103%), neg=0, invalid=1511 0111: dt=331.776005, rms=0.563 (0.702%), neg=0, invalid=1511 0112: dt=69.898007, rms=0.559 (0.678%), neg=0, invalid=1511 0113: dt=25.128029, rms=0.559 (0.046%), neg=0, invalid=1511 0114: dt=25.128029, rms=0.559 (0.059%), neg=0, invalid=1511 0115: dt=25.128029, rms=0.558 (0.110%), neg=0, invalid=1511 0116: dt=25.128029, rms=0.557 (0.175%), neg=0, invalid=1511 0117: dt=25.128029, rms=0.556 (0.220%), neg=0, invalid=1511 0118: dt=25.128029, rms=0.554 (0.247%), neg=0, invalid=1511 0119: dt=25.128029, rms=0.553 (0.246%), neg=0, invalid=1511 0120: dt=25.128029, rms=0.552 (0.256%), neg=0, invalid=1511 0121: dt=25.128029, rms=0.550 (0.265%), neg=0, invalid=1511 0122: dt=25.128029, rms=0.549 (0.263%), neg=0, invalid=1511 0123: dt=25.128029, rms=0.547 (0.254%), neg=0, invalid=1511 0124: dt=25.128029, rms=0.546 (0.240%), neg=0, invalid=1511 0125: dt=25.128029, rms=0.545 (0.229%), neg=0, invalid=1511 0126: dt=25.128029, rms=0.544 (0.230%), neg=0, invalid=1511 0127: dt=25.128029, rms=0.542 (0.235%), neg=0, invalid=1511 0128: dt=25.128029, rms=0.541 (0.213%), neg=0, invalid=1511 0129: dt=25.128029, rms=0.540 (0.200%), neg=0, invalid=1511 0130: dt=25.128029, rms=0.539 (0.192%), neg=0, invalid=1511 0131: dt=25.128029, rms=0.538 (0.186%), neg=0, invalid=1511 0132: dt=25.128029, rms=0.537 (0.177%), neg=0, invalid=1511 0133: dt=25.128029, rms=0.536 (0.154%), neg=0, invalid=1511 0134: dt=25.128029, rms=0.535 (0.143%), neg=0, invalid=1511 0135: dt=25.128029, rms=0.535 (0.140%), neg=0, invalid=1511 0136: dt=25.128029, rms=0.534 (0.137%), neg=0, invalid=1511 0137: dt=25.128029, rms=0.533 (0.132%), neg=0, invalid=1511 0138: dt=25.128029, rms=0.533 (0.122%), neg=0, invalid=1511 0139: dt=25.128029, rms=0.532 (0.114%), neg=0, invalid=1511 0140: dt=25.128029, rms=0.531 (0.114%), neg=0, invalid=1511 0141: dt=25.128029, rms=0.531 (0.120%), neg=0, invalid=1511 0142: dt=25.128029, rms=0.530 (0.123%), neg=0, invalid=1511 0143: dt=25.128029, rms=0.530 (0.113%), neg=0, invalid=1511 0144: dt=25.128029, rms=0.529 (0.094%), neg=0, invalid=1511 0145: dt=25.128029, rms=0.529 (0.082%), neg=0, invalid=1511 0146: dt=25.128029, rms=0.528 (0.077%), neg=0, invalid=1511 0147: dt=25.128029, rms=0.528 (0.080%), neg=0, invalid=1511 0148: dt=25.128029, rms=0.527 (0.088%), neg=0, invalid=1511 0149: dt=25.128029, rms=0.527 (0.083%), neg=0, invalid=1511 0150: dt=25.128029, rms=0.526 (0.076%), neg=0, invalid=1511 0151: dt=25.128029, rms=0.526 (0.071%), neg=0, invalid=1511 0152: dt=25.128029, rms=0.526 (0.071%), neg=0, invalid=1511 0153: dt=25.128029, rms=0.525 (0.073%), neg=0, invalid=1511 0154: dt=25.128029, rms=0.525 (0.068%), neg=0, invalid=1511 0155: dt=25.128029, rms=0.525 (0.067%), neg=0, invalid=1511 0156: dt=25.128029, rms=0.524 (0.062%), neg=0, invalid=1511 0157: dt=25.128029, rms=0.524 (0.064%), neg=0, invalid=1511 0158: dt=25.128029, rms=0.524 (0.059%), neg=0, invalid=1511 0159: dt=25.128029, rms=0.523 (0.054%), neg=0, invalid=1511 0160: dt=25.128029, rms=0.523 (0.052%), neg=0, invalid=1511 0161: dt=25.128029, rms=0.523 (0.056%), neg=0, invalid=1511 0162: dt=25.128029, rms=0.523 (0.052%), neg=0, invalid=1511 0163: dt=25.128029, rms=0.522 (0.050%), neg=0, invalid=1511 0164: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0165: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0166: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0167: dt=25.128029, rms=0.521 (0.044%), neg=0, invalid=1511 0168: dt=25.128029, rms=0.521 (0.043%), neg=0, invalid=1511 0169: dt=25.128029, rms=0.521 (0.044%), neg=0, invalid=1511 0170: dt=25.128029, rms=0.521 (0.038%), neg=0, invalid=1511 0171: dt=25.128029, rms=0.520 (0.036%), neg=0, invalid=1511 0172: dt=25.128029, rms=0.520 (0.038%), neg=0, invalid=1511 0173: dt=25.128029, rms=0.520 (0.040%), neg=0, invalid=1511 0174: dt=25.128029, rms=0.520 (0.038%), neg=0, invalid=1511 0175: dt=25.128029, rms=0.520 (0.032%), neg=0, invalid=1511 0176: dt=25.128029, rms=0.520 (0.031%), neg=0, invalid=1511 0177: dt=25.128029, rms=0.519 (0.036%), neg=0, invalid=1511 0178: dt=25.128029, rms=0.519 (0.037%), neg=0, invalid=1511 0179: dt=25.128029, rms=0.519 (0.038%), neg=0, invalid=1511 0180: dt=25.128029, rms=0.519 (0.036%), neg=0, invalid=1511 0181: dt=25.128029, rms=0.519 (0.025%), neg=0, invalid=1511 0182: dt=25.128029, rms=0.518 (0.023%), neg=0, invalid=1511 0183: dt=25.128029, rms=0.518 (0.024%), neg=0, invalid=1511 0184: dt=25.128029, rms=0.518 (0.032%), neg=0, invalid=1511 0185: dt=25.128029, rms=0.518 (0.043%), neg=0, invalid=1511 0186: dt=25.128029, rms=0.518 (0.041%), neg=0, invalid=1511 0187: dt=25.128029, rms=0.518 (0.030%), neg=0, invalid=1511 0188: dt=25.128029, rms=0.517 (0.022%), neg=0, invalid=1511 0189: dt=25.128029, rms=0.517 (0.015%), neg=0, invalid=1511 0190: dt=580.608009, rms=0.517 (0.079%), neg=0, invalid=1511 0191: dt=7.776000, rms=0.517 (-0.000%), neg=0, invalid=1511 0192: dt=7.776000, rms=0.517 (0.004%), neg=0, invalid=1511 0193: dt=7.776000, rms=0.517 (-0.010%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=1511 0194: dt=47.689071, rms=0.516 (0.131%), neg=0, invalid=1511 0195: dt=109.296352, rms=0.515 (0.283%), neg=0, invalid=1511 0196: dt=18.808524, rms=0.515 (0.039%), neg=0, invalid=1511 0197: dt=18.808524, rms=0.515 (0.005%), neg=0, invalid=1511 0198: dt=18.808524, rms=0.515 (-0.016%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=1511 0199: dt=35.201863, rms=0.525 (0.386%), neg=0, invalid=1511 0200: dt=84.272825, rms=0.519 (1.215%), neg=0, invalid=1511 0201: dt=27.028692, rms=0.517 (0.320%), neg=0, invalid=1511 0202: dt=47.856551, rms=0.514 (0.625%), neg=0, invalid=1511 0203: dt=32.000000, rms=0.512 (0.423%), neg=0, invalid=1511 0204: dt=36.705510, rms=0.511 (0.247%), neg=0, invalid=1511 0205: dt=23.097180, rms=0.509 (0.333%), neg=0, invalid=1511 0206: dt=12.611658, rms=0.508 (0.077%), neg=0, invalid=1511 0207: dt=179.200003, rms=0.505 (0.729%), neg=0, invalid=1511 0208: dt=33.050655, rms=0.503 (0.390%), neg=0, invalid=1511 0209: dt=20.841661, rms=0.502 (0.150%), neg=0, invalid=1511 0210: dt=36.934922, rms=0.501 (0.182%), neg=0, invalid=1511 0211: dt=9.773344, rms=0.501 (0.037%), neg=0, invalid=1511 0212: dt=9.773344, rms=0.501 (0.038%), neg=0, invalid=1511 0213: dt=9.773344, rms=0.501 (0.032%), neg=0, invalid=1511 0214: dt=9.773344, rms=0.500 (0.076%), neg=0, invalid=1511 0215: dt=9.773344, rms=0.500 (0.129%), neg=0, invalid=1511 0216: dt=9.773344, rms=0.499 (0.127%), neg=0, invalid=1511 0217: dt=9.773344, rms=0.498 (0.121%), neg=0, invalid=1511 0218: dt=9.773344, rms=0.498 (0.101%), neg=0, invalid=1511 0219: dt=9.773344, rms=0.497 (0.120%), neg=0, invalid=1511 0220: dt=9.773344, rms=0.496 (0.161%), neg=0, invalid=1511 0221: dt=9.773344, rms=0.496 (0.169%), neg=0, invalid=1511 0222: dt=9.773344, rms=0.495 (0.144%), neg=0, invalid=1511 0223: dt=9.773344, rms=0.494 (0.111%), neg=0, invalid=1511 0224: dt=9.773344, rms=0.494 (0.111%), neg=0, invalid=1511 0225: dt=9.773344, rms=0.493 (0.134%), neg=0, invalid=1511 0226: dt=9.773344, rms=0.492 (0.141%), neg=0, invalid=1511 0227: dt=9.773344, rms=0.492 (0.116%), neg=0, invalid=1511 0228: dt=9.773344, rms=0.491 (0.089%), neg=0, invalid=1511 0229: dt=9.773344, rms=0.491 (0.081%), neg=0, invalid=1511 0230: dt=9.773344, rms=0.490 (0.097%), neg=0, invalid=1511 0231: dt=9.773344, rms=0.490 (0.101%), neg=0, invalid=1511 0232: dt=9.773344, rms=0.490 (0.079%), neg=0, invalid=1511 0233: dt=9.773344, rms=0.489 (0.063%), neg=0, invalid=1511 0234: dt=9.773344, rms=0.489 (0.053%), neg=0, invalid=1511 0235: dt=9.773344, rms=0.489 (0.064%), neg=0, invalid=1511 0236: dt=9.773344, rms=0.488 (0.072%), neg=0, invalid=1511 0237: dt=9.773344, rms=0.488 (0.059%), neg=0, invalid=1511 0238: dt=9.773344, rms=0.488 (0.043%), neg=0, invalid=1511 0239: dt=9.773344, rms=0.488 (0.038%), neg=0, invalid=1511 0240: dt=9.773344, rms=0.487 (0.048%), neg=0, invalid=1511 0241: dt=9.773344, rms=0.487 (0.053%), neg=0, invalid=1511 0242: dt=9.773344, rms=0.487 (0.043%), neg=0, invalid=1511 0243: dt=9.773344, rms=0.487 (0.030%), neg=0, invalid=1511 0244: dt=9.773344, rms=0.487 (0.031%), neg=0, invalid=1511 0245: dt=9.773344, rms=0.486 (0.044%), neg=0, invalid=1511 0246: dt=9.773344, rms=0.486 (0.053%), neg=0, invalid=1511 0247: dt=9.773344, rms=0.486 (0.032%), neg=0, invalid=1511 0248: dt=9.773344, rms=0.486 (0.024%), neg=0, invalid=1511 0249: dt=9.773344, rms=0.486 (0.022%), neg=0, invalid=1511 0250: dt=102.400002, rms=0.486 (0.049%), neg=0, invalid=1511 0251: dt=1.600000, rms=0.486 (-0.008%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=1511 0252: dt=15.569267, rms=0.485 (0.141%), neg=0, invalid=1511 0253: dt=24.738315, rms=0.484 (0.222%), neg=0, invalid=1511 0254: dt=6.809498, rms=0.484 (0.031%), neg=0, invalid=1511 0255: dt=6.809498, rms=0.484 (0.019%), neg=0, invalid=1511 0256: dt=6.809498, rms=0.484 (0.017%), neg=0, invalid=1511 0257: dt=6.809498, rms=0.483 (0.049%), neg=0, invalid=1511 0258: dt=6.809498, rms=0.483 (0.071%), neg=0, invalid=1511 0259: dt=6.809498, rms=0.483 (0.052%), neg=0, invalid=1511 0260: dt=6.809498, rms=0.483 (0.022%), neg=0, invalid=1511 0261: dt=6.809498, rms=0.483 (0.009%), neg=0, invalid=1511 0262: dt=44.800001, rms=0.482 (0.039%), neg=0, invalid=1511 0263: dt=2.800000, rms=0.482 (-0.001%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0264: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=1511 0265: dt=0.150000, rms=0.510 (-0.008%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0266: dt=0.000000, rms=0.510 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=1511 0267: dt=2.168286, rms=0.553 (1.795%), neg=0, invalid=1511 0268: dt=1.170096, rms=0.553 (0.134%), neg=0, invalid=1511 0269: dt=0.384000, rms=0.553 (0.009%), neg=0, invalid=1511 0270: dt=0.384000, rms=0.553 (-0.002%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=1511 0271: dt=1.883680, rms=0.551 (0.227%), neg=0, invalid=1511 0272: dt=0.448000, rms=0.551 (0.014%), neg=0, invalid=1511 0273: dt=0.448000, rms=0.551 (0.006%), neg=0, invalid=1511 0274: dt=0.448000, rms=0.551 (-0.013%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0275: dt=0.448000, rms=0.496 (2.606%), neg=0, invalid=1511 0276: dt=1.536000, rms=0.487 (1.924%), neg=0, invalid=1511 0277: dt=0.384000, rms=0.487 (0.076%), neg=0, invalid=1511 0278: dt=0.000000, rms=0.487 (0.007%), neg=0, invalid=1511 0279: dt=0.050000, rms=0.487 (-0.001%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=1511 0280: dt=0.448000, rms=0.483 (0.634%), neg=0, invalid=1511 0281: dt=0.448000, rms=0.483 (0.069%), neg=0, invalid=1511 0282: dt=0.448000, rms=0.483 (0.062%), neg=0, invalid=1511 0283: dt=0.448000, rms=0.483 (0.052%), neg=0, invalid=1511 0284: dt=0.448000, rms=0.482 (0.053%), neg=0, invalid=1511 0285: dt=0.448000, rms=0.482 (0.048%), neg=0, invalid=1511 0286: dt=0.448000, rms=0.482 (0.044%), neg=0, invalid=1511 0287: dt=0.448000, rms=0.481 (0.080%), neg=0, invalid=1511 0288: dt=0.448000, rms=0.481 (0.107%), neg=0, invalid=1511 0289: dt=0.448000, rms=0.480 (0.119%), neg=0, invalid=1511 0290: dt=0.448000, rms=0.480 (0.120%), neg=0, invalid=1511 0291: dt=0.448000, rms=0.480 (0.011%), neg=0, invalid=1511 0292: dt=0.448000, rms=0.480 (0.013%), neg=0, invalid=1511 0293: dt=0.448000, rms=0.480 (0.027%), neg=0, invalid=1511 0294: dt=0.448000, rms=0.479 (0.029%), neg=0, invalid=1511 0295: dt=0.056000, rms=0.479 (0.002%), neg=0, invalid=1511 0296: dt=0.056000, rms=0.479 (0.003%), neg=0, invalid=1511 0297: dt=0.056000, rms=0.479 (0.001%), neg=0, invalid=1511 0298: dt=0.448000, rms=0.479 (0.009%), neg=0, invalid=1511 0299: dt=0.001750, rms=0.479 (-0.001%), neg=0, invalid=1511 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=1511 0300: dt=129.472002, rms=0.477 (0.030%), neg=0, invalid=1511 0301: dt=129.472002, rms=0.477 (0.057%), neg=0, invalid=1511 0302: dt=32.368000, rms=0.477 (0.009%), neg=0, invalid=1511 0303: dt=32.368000, rms=0.476 (0.008%), neg=0, invalid=1511 0304: dt=16.184000, rms=0.476 (0.004%), neg=0, invalid=1511 0305: dt=4.046000, rms=0.476 (0.001%), neg=0, invalid=1511 0306: dt=0.505750, rms=0.476 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=1511 0307: dt=129.472002, rms=0.476 (0.169%), neg=0, invalid=1511 0308: dt=295.936004, rms=0.475 (0.056%), neg=0, invalid=1511 0309: dt=129.472002, rms=0.475 (0.060%), neg=0, invalid=1511 0310: dt=92.480001, rms=0.475 (0.019%), neg=0, invalid=1511 0311: dt=92.480001, rms=0.475 (0.015%), neg=0, invalid=1511 0312: dt=92.480001, rms=0.475 (0.024%), neg=0, invalid=1511 0313: dt=92.480001, rms=0.475 (0.035%), neg=0, invalid=1511 0314: dt=92.480001, rms=0.474 (0.037%), neg=0, invalid=1511 0315: dt=92.480001, rms=0.474 (0.039%), neg=0, invalid=1511 0316: dt=92.480001, rms=0.474 (0.037%), neg=0, invalid=1511 0317: dt=92.480001, rms=0.474 (0.035%), neg=0, invalid=1511 0318: dt=92.480001, rms=0.474 (0.034%), neg=0, invalid=1511 0319: dt=92.480001, rms=0.474 (0.030%), neg=0, invalid=1511 0320: dt=92.480001, rms=0.474 (0.027%), neg=0, invalid=1511 0321: dt=92.480001, rms=0.473 (0.025%), neg=0, invalid=1511 0322: dt=92.480001, rms=0.473 (0.023%), neg=0, invalid=1511 0323: dt=295.936004, rms=0.473 (0.009%), neg=0, invalid=1511 0324: dt=295.936004, rms=0.473 (-0.031%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0325: dt=36.288001, rms=0.473 (0.063%), neg=0, invalid=1511 0326: dt=14.141785, rms=0.473 (0.020%), neg=0, invalid=1511 0327: dt=7.070892, rms=0.473 (0.010%), neg=0, invalid=1511 0328: dt=1.767723, rms=0.473 (0.003%), neg=0, invalid=1511 0329: dt=0.220965, rms=0.473 (0.000%), neg=0, invalid=1511 0330: dt=0.101250, rms=0.473 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0331: dt=0.035438, rms=0.473 (0.000%), neg=0, invalid=1511 0332: dt=0.035438, rms=0.473 (0.000%), neg=0, invalid=1511 0333: dt=0.008859, rms=0.473 (0.000%), neg=0, invalid=1511 0334: dt=0.002215, rms=0.473 (0.000%), neg=0, invalid=1511 0335: dt=0.000017, rms=0.473 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0336: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0337: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=1511 0338: dt=4.032000, rms=0.467 (1.406%), neg=0, invalid=1511 0339: dt=4.032000, rms=0.463 (0.974%), neg=0, invalid=1511 0340: dt=11.520000, rms=0.454 (1.818%), neg=0, invalid=1511 0341: dt=1.008000, rms=0.454 (0.059%), neg=0, invalid=1511 0342: dt=2.880000, rms=0.453 (0.173%), neg=0, invalid=1511 0343: dt=4.032000, rms=0.452 (0.212%), neg=0, invalid=1511 0344: dt=1.008000, rms=0.452 (0.042%), neg=0, invalid=1511 0345: dt=1.008000, rms=0.452 (0.040%), neg=0, invalid=1511 0346: dt=1.008000, rms=0.451 (0.075%), neg=0, invalid=1511 0347: dt=1.008000, rms=0.451 (0.102%), neg=0, invalid=1511 0348: dt=1.008000, rms=0.450 (0.121%), neg=0, invalid=1511 0349: dt=1.008000, rms=0.450 (0.132%), neg=0, invalid=1511 0350: dt=1.008000, rms=0.449 (0.138%), neg=0, invalid=1511 0351: dt=1.008000, rms=0.449 (0.137%), neg=0, invalid=1511 0352: dt=1.008000, rms=0.448 (0.131%), neg=0, invalid=1511 0353: dt=1.008000, rms=0.447 (0.121%), neg=0, invalid=1511 0354: dt=1.008000, rms=0.447 (0.108%), neg=0, invalid=1511 0355: dt=1.008000, rms=0.447 (0.094%), neg=0, invalid=1511 0356: dt=1.008000, rms=0.446 (0.080%), neg=0, invalid=1511 0357: dt=1.008000, rms=0.446 (0.065%), neg=0, invalid=1511 0358: dt=1.008000, rms=0.446 (-0.006%), neg=0, invalid=1511 0359: dt=0.000000, rms=0.446 (-0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=1511 0360: dt=4.032000, rms=0.445 (0.220%), neg=0, invalid=1511 0361: dt=4.032000, rms=0.444 (0.121%), neg=0, invalid=1511 0362: dt=13.824000, rms=0.444 (0.150%), neg=0, invalid=1511 0363: dt=4.032000, rms=0.444 (0.019%), neg=0, invalid=1511 0364: dt=4.032000, rms=0.444 (0.017%), neg=0, invalid=1511 0365: dt=4.032000, rms=0.443 (0.030%), neg=0, invalid=1511 0366: dt=4.032000, rms=0.443 (0.034%), neg=0, invalid=1511 0367: dt=4.032000, rms=0.443 (0.034%), neg=0, invalid=1511 0368: dt=4.032000, rms=0.443 (0.040%), neg=0, invalid=1511 0369: dt=4.032000, rms=0.443 (0.052%), neg=0, invalid=1511 0370: dt=4.032000, rms=0.442 (0.070%), neg=0, invalid=1511 0371: dt=4.032000, rms=0.442 (0.091%), neg=0, invalid=1511 0372: dt=4.032000, rms=0.442 (0.104%), neg=0, invalid=1511 0373: dt=4.032000, rms=0.441 (0.111%), neg=0, invalid=1511 0374: dt=4.032000, rms=0.441 (0.110%), neg=0, invalid=1511 0375: dt=4.032000, rms=0.440 (0.102%), neg=0, invalid=1511 0376: dt=4.032000, rms=0.440 (0.088%), neg=0, invalid=1511 0377: dt=4.032000, rms=0.439 (0.073%), neg=0, invalid=1511 0378: dt=4.032000, rms=0.439 (0.058%), neg=0, invalid=1511 0379: dt=4.032000, rms=0.439 (0.044%), neg=0, invalid=1511 0380: dt=4.032000, rms=0.439 (0.034%), neg=0, invalid=1511 0381: dt=4.032000, rms=0.439 (0.027%), neg=0, invalid=1511 0382: dt=4.032000, rms=0.439 (0.021%), neg=0, invalid=1511 0383: dt=4.032000, rms=0.439 (0.018%), neg=0, invalid=1511 0384: dt=16.128000, rms=0.438 (0.010%), neg=0, invalid=1511 0385: dt=16.128000, rms=0.438 (0.000%), neg=0, invalid=1511 0386: dt=16.128000, rms=0.438 (-0.005%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=1511 0387: dt=0.000000, rms=0.445 (-0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=1511 0388: dt=0.000000, rms=0.445 (0.000%), neg=0, invalid=1511 0389: dt=0.100000, rms=0.445 (-0.069%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=1511 0390: dt=0.112000, rms=0.432 (0.533%), neg=0, invalid=1511 0391: dt=0.112000, rms=0.430 (0.403%), neg=0, invalid=1511 0392: dt=0.028000, rms=0.430 (0.078%), neg=0, invalid=1511 0393: dt=0.112000, rms=0.428 (0.291%), neg=0, invalid=1511 0394: dt=0.112000, rms=0.427 (0.226%), neg=0, invalid=1511 0395: dt=0.112000, rms=0.427 (0.178%), neg=0, invalid=1511 0396: dt=0.028000, rms=0.427 (0.035%), neg=0, invalid=1511 0397: dt=0.028000, rms=0.426 (0.034%), neg=0, invalid=1511 0398: dt=0.028000, rms=0.426 (0.062%), neg=0, invalid=1511 0399: dt=0.028000, rms=0.426 (0.085%), neg=0, invalid=1511 0400: dt=0.028000, rms=0.425 (0.100%), neg=0, invalid=1511 0401: dt=0.028000, rms=0.425 (0.110%), neg=0, invalid=1511 0402: dt=0.028000, rms=0.424 (0.112%), neg=0, invalid=1511 0403: dt=0.014000, rms=0.424 (0.005%), neg=0, invalid=1511 0404: dt=0.014000, rms=0.424 (0.005%), neg=0, invalid=1511 0405: dt=0.028000, rms=0.424 (0.010%), neg=0, invalid=1511 0406: dt=0.028000, rms=0.424 (0.010%), neg=0, invalid=1511 0407: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 0408: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 0409: dt=0.007000, rms=0.424 (0.005%), neg=0, invalid=1511 0410: dt=0.007000, rms=0.424 (0.006%), neg=0, invalid=1511 0411: dt=0.007000, rms=0.424 (0.008%), neg=0, invalid=1511 0412: dt=0.007000, rms=0.424 (0.009%), neg=0, invalid=1511 0413: dt=0.007000, rms=0.424 (0.011%), neg=0, invalid=1511 0414: dt=0.007000, rms=0.424 (0.012%), neg=0, invalid=1511 0415: dt=0.007000, rms=0.424 (0.012%), neg=0, invalid=1511 0416: dt=0.007000, rms=0.424 (0.013%), neg=0, invalid=1511 0417: dt=0.007000, rms=0.424 (0.013%), neg=0, invalid=1511 0418: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=1511 0419: dt=0.024000, rms=0.424 (0.044%), neg=0, invalid=1511 0420: dt=0.028000, rms=0.423 (0.049%), neg=0, invalid=1511 0421: dt=0.028000, rms=0.423 (0.045%), neg=0, invalid=1511 0422: dt=0.028000, rms=0.423 (0.042%), neg=0, invalid=1511 0423: dt=0.028000, rms=0.423 (0.077%), neg=0, invalid=1511 0424: dt=0.028000, rms=0.423 (0.035%), neg=0, invalid=1511 0425: dt=0.028000, rms=0.422 (0.063%), neg=0, invalid=1511 0426: dt=0.028000, rms=0.422 (0.084%), neg=0, invalid=1511 0427: dt=0.028000, rms=0.422 (0.097%), neg=0, invalid=1511 0428: dt=0.028000, rms=0.421 (0.018%), neg=0, invalid=1511 0429: dt=0.028000, rms=0.421 (0.032%), neg=0, invalid=1511 0430: dt=0.028000, rms=0.421 (0.044%), neg=0, invalid=1511 0431: dt=0.028000, rms=0.421 (0.013%), neg=0, invalid=1511 0432: dt=0.028000, rms=0.421 (0.024%), neg=0, invalid=1511 0433: dt=0.028000, rms=0.421 (0.033%), neg=0, invalid=1511 0434: dt=0.028000, rms=0.421 (0.009%), neg=0, invalid=1511 0435: dt=0.028000, rms=0.421 (0.018%), neg=0, invalid=1511 0436: dt=0.028000, rms=0.421 (0.024%), neg=0, invalid=1511 0437: dt=0.028000, rms=0.421 (0.029%), neg=0, invalid=1511 0438: dt=0.014000, rms=0.421 (0.003%), neg=0, invalid=1511 0439: dt=0.014000, rms=0.421 (0.006%), neg=0, invalid=1511 0440: dt=0.014000, rms=0.420 (0.003%), neg=0, invalid=1511 0441: dt=0.112000, rms=0.420 (0.023%), neg=0, invalid=1511 0442: dt=0.096000, rms=0.420 (0.016%), neg=0, invalid=1511 0443: dt=0.048000, rms=0.420 (0.007%), neg=0, invalid=1511 0444: dt=0.024000, rms=0.420 (0.00Segmentation fault ERROR: mri_ca_register with non-zero status Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Mon Feb 5 23:16:19 CST 2007 New invocation of recon-all Thu Feb 8 18:48:51 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 /usr/local/freesurfer/bin//recon-all -subjid P44W_10588_L1 -autorecon-all subjid P44W_10588_L1 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-rh9-stable-pub-v3.0.4 Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc unlimited ######################################## program versions used $Id: recon-all,v 1.17.2.15 2006/11/21 04:58:13 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.4 2006/01/01 21:56:44 greve Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:51-GMT CVS: $Id: mri_convert.c,v 1.121.2.1 2006/08/28 18:00:04 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ mri_convert --version $ # $Id: mritotal.in,v 1.12 2004/02/12 05:55:18 rotor Exp $ Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mri_normalize.c,v 1.44.2.2 2006/06/28 23:38:13 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.5 2006/07/18 18:26:01 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:52-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mri_label2label.c,v 1.23.2.1 2006/09/20 20:42:55 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mri_ca_register.c,v 1.48.2.7 2006/10/24 01:48:52 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 07/02/09-00:48:53-GMT CVS: $Id: mri_ca_label.c,v 1.68.2.2 2006/08/16 00:18:42 nicks Exp $ User: binyam Machine: ConnorLabUbuntu Platform: Linux PlatformVersion: 2.6.15-27-386 CompilerName: GCC CompilerVersion: 30200 ####################################### GCA RB_all_2006-02-15.gca GCASkull RB_all_withskull_2006-02-15.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /usr/local/freesurfer/ #-------------------------------------------- #@# MotionCor Thu Feb 8 18:48:54 CST 2007 Found 4 runs /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1 mri_motion_correct.fsl -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -wild /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz tmpdir is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz Thu Feb 8 18:49:13 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/001.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz Thu Feb 8 18:49:15 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/002.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz Thu Feb 8 18:49:18 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/003.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz Thu Feb 8 18:49:20 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img -odt float reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig/004.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) changing data type from 4 to 3 (noscale = 0)... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img... Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img Thu Feb 8 18:49:23 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Thu Feb 8 18:49:23 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Thu Feb 8 18:49:23 CST 2007 Ended at Thu Feb 8 18:53:05 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img Thu Feb 8 18:53:05 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Thu Feb 8 18:53:05 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Thu Feb 8 18:53:05 CST 2007 Ended at Thu Feb 8 18:56:44 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img ----------------------------------------- Motion Correcting /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img Thu Feb 8 18:56:44 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 fsl_rigid_register -maxangle 90 -r /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -i /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img -o /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img -tmpdir /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493 -cleanup \n\n $Id: fsl_rigid_register,v 1.14 2006/02/13 20:13:19 greve Exp $ Thu Feb 8 18:56:44 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img Reference is analyze, not converting Input is analyze, not converting Output is analyze, not converting -------------------------------------- /usr/local/freesurfer/subjects/P44W_10588_L1 calling eval flirt -in /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.hdr -out /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.hdr -omat /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.fslmat WARNING: Both reference and input images have an sform matrix set The output image will use the sform from the reference image Started at Thu Feb 8 18:56:44 CST 2007 Ended at Thu Feb 8 19:00:23 CST 2007 fsl_rigid_register Done To check results, run: tkmedit -f /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img -aux /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img mv /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/resampled.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img ----------------------------------------- Averaging Thu Feb 8 19:00:23 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 inhibiting isotropic volume interpolation 1 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-1.img... 2 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-2.img... 3 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-3.img... 4 of 4: reading /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/cor-4.img... writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/avgvol.img... alignment and averaging took 0 minutes and 32 seconds. Analyze Output Matrix 0.016 -0.005 -1.250 101.045; -1.000 -0.000 -0.020 133.604; 0.000 -1.000 0.007 96.461; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting Average to output Thu Feb 8 19:00:55 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/avgvol.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -tr 1900 -te 3.93 -TI 1100 -flip_angle 0.261799 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/avgvol.img /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz -tr 1900 -te 3.93 -TI 1100 -flip_angle 0.261799 reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/tmp-mri_motion_correct.fsl-6493/avgvol.img... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) writing to /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz... ----------------------------------------- Started at: Thu Feb 8 18:48:58 CST 2007 Ended at: Thu Feb 8 19:01:03 CST 2007 mri_motion_correct.fsl: done /usr/local/freesurfer/subjects/P44W_10588_L1 mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/P44W_10588_L1/mri/rawavg.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (0.0157073, -0.999877, 6.37293e-08) j_ras = (-0.00523535, -8.23071e-05, -0.999986) k_ras = (-0.999863, -0.0157071, 0.00523596) Original Data has (1, 1, 1.25) mm size and (224, 256, 160) 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 /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/P44W_10588_L1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz /usr/local/freesurfer/subjects/P44W_10588_L1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Thu Feb 8 19:01:22 CST 2007 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/P44W_10588_L1/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 1.3.2.1 2006/11/24 20:16:38 nicks Exp $ Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux Thu Feb 8 19:01:22 CST 2007 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.7117 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7117/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.7117/nu0.mnc reading from orig.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) writing to ./tmp.mri_nu_correct.mni.7117/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Feb 8 19:01:30 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7117/nu0.mnc ./tmp.mri_nu_correct.mni.7117/nu1.mnc [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-08 19:01:30] 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 /var/tmp/nu_correct_7171/ ./tmp.mri_nu_correct.mni.7117/nu0.mnc ./tmp.mri_nu_correct.mni.7117/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() Number of iterations: 43 CV of field change: 0.000984685 [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-08 19:02:30] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7117/nu0.mnc /var/tmp/nu_correct_7171//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 Thu Feb 8 19:02:37 CST 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.7117/nu1.mnc ./tmp.mri_nu_correct.mni.7117/nu2.mnc [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-08 19:02:37] 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 /var/tmp/nu_correct_7755/ ./tmp.mri_nu_correct.mni.7117/nu1.mnc ./tmp.mri_nu_correct.mni.7117/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Not implemented yet in cache_volume_range_has_changed() Number of iterations: 40 CV of field change: 0.000989415 [binyam@ConnorLabUbuntu:/usr/local/freesurfer/subjects/P44W_10588_L1/mri/] [2007-02-08 19:03:34] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.7117/nu1.mnc /var/tmp/nu_correct_7755//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.7117/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.7117/nu2.mnc nu.mgz --like orig.mgz reading from ./tmp.mri_nu_correct.mni.7117/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... Thu Feb 8 19:03:56 CST 2007 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Thu Feb 8 19:03:56 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/P44W_10588_L1/mri /usr/local/freesurfer/bin//talairach --i nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.2 2005/12/12 23:04:35 greve Exp $ Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux Thu Feb 8 19:03:56 CST 2007 tmpdir is transforms/tmp.talairach.8335 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_convert nu.mgz transforms/tmp.talairach.8335/src.mnc mri_convert nu.mgz transforms/tmp.talairach.8335/src.mnc reading from nu.mgz... TR=1900.00, TE=3.93, TI=1100.00, flip angle=15.00 i_ras = (-1, 1.79449e-10, 3.33208e-10) j_ras = (-1.30826e-10, 3.1719e-15, -1) k_ras = (8.80186e-10, 1, 1.66687e-13) writing to transforms/tmp.talairach.8335/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.8335/src.mnc transforms/talairach.auto.xfm Thu Feb 8 19:04:39 CST 2007 talairach done #-------------------------------------------- #@# Intensity Normalization Thu Feb 8 19:04:39 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.103 0.046 -0.012 -0.075; -0.041 1.039 0.164 -19.026; 0.019 -0.172 1.099 23.452; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 4 minutes and 47 seconds. white matter peak found at 110 gm peak at 83 (83), valley at 49 (49) csf peak at 34, setting threshold to 66 white matter peak found at 110 gm peak at 83 (83), valley at 42 (42) csf peak at 42, setting threshold to 69 #-------------------------------------------- #@# Skull Stripping Thu Feb 8 19:09:28 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz T1.mgz brainmask.auto.mgz ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz If this is incorrect, please exit with CTL-C *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 247966 Find the largest 110-component... heap usage = 280088 Kbytes. current max segment has 218351 voxels removing small segments (less than 1 percent of maxarea). heap usage = 137764 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 218351 voxels first estimation of the COG coord: x=128 y=111 z=111 r=88 first estimation of the main basin volume: 2877798 voxels global maximum in x=157, y=109, z=69, Imax=255 CSF=19, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 done Analyze main basin size= 1750515 voxels, voxel volume =1.000 = 1750515 mmm3 = 1750.515 cm3 done PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=109, z=108, r=9753 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=58, TRANSITION=62, GM_MIN=66, GM=84 after analyzing : CSF_MAX=58, TRANSITION=64, GM_MIN=66, GM=69 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* No Rigid alignment: Atlas Mode Off before rotation: sse = 2.05, sigma = 3.74 after rotation: sse = 2.05, sigma = 3.74 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.08, its var is 2.96 before Erosion-Dilatation 0.88% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1698687 voxels, voxel volume = 1.000 mm3 = 1698687 mmm3 = 1698.687 cm3 ****************************** Save...done Keeping brain edits brainmask.auto.mgz brainmask.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... #------------------------------------- #@# EM Registration Thu Feb 8 19:10:59 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_em_register -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... total sample mean = 87.9 (483 zeros) register_mri: find_optimal_transform find_optimal_transform: nsamples 2242, passno 0, spacing 8 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-2.8, 9.7, -5.1): log p = -15685.1 Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-15685.1 (thresh=-15669.4) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-12180.5, old_max_log_p =-12180.5 (thresh=-12168.3) 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... fp = 12131.479492, fret = 12131.479492, ftol = 0.000010, EPS = 0.000000 dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.05469 0.00000 0.00000 -9.92348; 0.00000 1.05216 0.14787 -12.30865; 0.00000 -0.13917 0.99027 11.10739; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... pass 3 through quasi-newton minimization... pass 4 through quasi-newton minimization... pass 5 through quasi-newton minimization... pass 6 through quasi-newton minimization... freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 initial log_p = -31639.6 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** reducing scale to 0.2500 *********************************************** Computing MAP estimate using 2242 samples... *********************************************** dfp_em_step_func: 002: -log(p) = 12180.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 003: -log(p) = 12176.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 004: -log(p) = 12144.9 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 005: -log(p) = 12131.5 after pass:transform: ( 1.05, 0.00, -0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) outof QuasiNewtonEMA: 007: -log(p) = 12131.5 tol 0.000010 Resulting transform: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -12180.5 (old=-31639.6) transform before final EM align: 1.055 0.000 0.000 -9.923; 0.000 1.052 0.148 -12.309; 0.000 -0.139 0.990 11.107; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 006: -log(p) = 1488031.5 after pass:transform: ( 1.05, 0.00, 0.00, -9.92) ( 0.00, 1.05, 0.15, -12.31) ( 0.00, -0.14, 0.99, 11.11) dfp_em_step_func: 007: -log(p) = 1474529.9 after pass:transform: ( 1.06, 0.00, 0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.01, -0.13, 1.00, 11.11) dfp_em_step_func: 008: -log(p) = 1463433.4 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( 0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 009: -log(p) = 1456579.2 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 010: -log(p) = 1455069.6 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) dfp_em_step_func: 011: -log(p) = 1454569.5 after pass:transform: ( 1.06, 0.00, -0.00, -9.92) ( -0.00, 1.06, 0.15, -12.31) ( 0.00, -0.13, 1.00, 11.11) outof QuasiNewtonEMA: 013: -log(p) = 1454455.0 tol 0.000000 final transform: 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 5 minutes and 56 seconds. #-------------------------------------- #@# CA Normalize Thu Feb 8 19:16:55 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.059 0.003 -0.002 -9.923; -0.000 1.056 0.152 -12.309; 0.003 -0.134 0.997 11.107; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... resetting wm mean[0]: 109 --> 116 resetting gm mean[0]: 68 --> 68 input volume #1 is the most T1-like using real data threshold=45.0 using (105, 89, 119) as brain centroid... mean wm in atlas = 116, using box (89,74,99) --> (120, 103,139) to find MRI wm before smoothing, mri peak at 116 after smoothing, mri peak at 114, scaling input intensities by 1.018 scaling channel 0 by 1.01754 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (128, 48, 31) --> (191, 153, 196) Left_Cerebral_White_Matter: limiting intensities to 100.0 --> 118.0 688 of 3149 (21.8%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (68, 48, 31) --> (128, 153, 197) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 119.0 413 of 3134 (13.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (130, 131, 57) --> (174, 170, 111) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 112.0 70 of 199 (35.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (85, 133, 55) --> (128, 170, 111) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 110.0 59 of 188 (31.4%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (111, 118, 92) --> (143, 185, 122) Brain_Stem: limiting intensities to 95.0 --> 106.0 106 of 264 (40.2%) samples deleted using 6934 total control points for intensity normalization... bias field = 1.016 +- 0.060 24 of 5598 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 20 seconds. #-------------------------------------- #@# CA Reg Thu Feb 8 19:18:14 CST 2007 /usr/local/freesurfer/subjects/P44W_10588_L1/mri mri_ca_register -align -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz /usr/local/freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.m3z renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 not handling expanded ventricles... using MR volume brainmask.mgz to mask input volume... using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) renormalizing by structure alignment.... renormalizing input #0 aligning Left_Pallidum... gca peak = 0.11705 (100) mri peak = 0.15616 (105) Left_Pallidum (13): linear fit = 0.98 x + 0.0 (650 voxels, overlap=0.725) aligning Right_Pallidum... gca peak = 0.13501 (106) mri peak = 0.14880 (104) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (996 voxels, overlap=0.633) aligning Right_Cerebral_White_Matter... gca peak = 0.05652 (116) mri peak = 0.07673 (115) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (109779 voxels, overlap=0.532) aligning Left_Cerebral_White_Matter... gca peak = 0.05682 (116) mri peak = 0.05484 (115) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (129515 voxels, overlap=0.428) aligning Left_Lateral_Ventricle... gca peak = 0.05153 (25) mri peak = 0.04526 (33) Left_Lateral_Ventricle (4): linear fit = 1.55 x + 0.0 (5475 voxels, overlap=0.181) aligning Right_Lateral_Ventricle... gca peak = 0.07557 (30) mri peak = 0.06721 (31) Right_Lateral_Ventricle (43): linear fit = 1.30 x + 0.0 (5308 voxels, overlap=0.203) aligning Right_Hippocampus... gca peak = 0.14805 (66) mri peak = 0.10387 (80) Right_Hippocampus (53): linear fit = 1.17 x + 0.0 (2085 voxels, overlap=0.058) aligning Left_Hippocampus... gca peak = 0.17297 (66) mri peak = 0.09064 (81) Left_Hippocampus (17): linear fit = 1.20 x + 0.0 (1694 voxels, overlap=0.057) aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.02939 (84) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.03178 (81) Right_Cerebral_Cortex (42): linear fit = 1.23 x + 0.0 (142002 voxels, overlap=0.108) aligning Right_Caudate... gca peak = 0.07786 (81) mri peak = 0.14952 (93) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1616 voxels, overlap=0.125) aligning Left_Caudate... gca peak = 0.07814 (81) mri peak = 0.11678 (90) Left_Caudate (11): linear fit = 1.10 x + 0.0 (1408 voxels, overlap=0.372) aligning Left_Cerebellum_Cortex... gca peak = 0.06033 (63) mri peak = 0.06077 (86) overlap = 0.000534633, overlap_threshold = 0.001 insufficient overlap 0.0005 in histograms - rejecting aligning Right_Cerebellum_Cortex... gca peak = 0.05990 (64) mri peak = 0.06449 (83) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (35986 voxels, overlap=0.008) aligning Left_Cerebellum_White_Matter... gca peak = 0.09299 (92) mri peak = 0.06522 (103) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (16273 voxels, overlap=0.585) aligning Right_Cerebellum_White_Matter... gca peak = 0.08899 (93) mri peak = 0.07489 (101) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (13032 voxels, overlap=0.731) aligning Left_Amygdala... gca peak = 0.13911 (71) mri peak = 0.13070 (79) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (911 voxels, overlap=0.047) aligning Right_Amygdala... gca peak = 0.15703 (65) mri peak = 0.11577 (80) Right_Amygdala (54): linear fit = 1.20 x + 0.0 (973 voxels, overlap=0.012) aligning Left_Thalamus_Proper... gca peak = 0.06537 (100) mri peak = 0.09795 (103) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3335 voxels, overlap=0.520) aligning Right_Thalamus_Proper... gca peak = 0.07019 (99) mri peak = 0.11165 (102) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (3212 voxels, overlap=0.501) aligning Left_Putamen... gca peak = 0.09468 (90) mri peak = 0.13402 (94) Left_Putamen (12): linear fit = 1.08 x + 0.0 (3118 voxels, overlap=0.440) aligning Right_Putamen... gca peak = 0.07184 (82) mri peak = 0.11033 (94) Right_Putamen (51): linear fit = 1.08 x + 0.0 (2899 voxels, overlap=0.476) aligning Brain_Stem... gca peak = 0.05597 (80) mri peak = 0.11599 (98) Brain_Stem (16): linear fit = 1.02 x + 0.0 (13631 voxels, overlap=0.309) aligning Right_VentralDC... gca peak = 0.05879 (97) mri peak = 0.08127 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (2695 voxels, overlap=0.476) aligning Left_VentralDC... gca peak = 0.06932 (98) mri peak = 0.07580 (105) Left_VentralDC (28): linear fit = 0.98 x + 0.0 (2707 voxels, overlap=0.524) aligning Third_Ventricle... gca peak = 0.10105 (38) mri peak = 0.06389 (32) Third_Ventricle (14): linear fit = 0.93 x + 0.0 (410 voxels, overlap=0.394) aligning Fourth_Ventricle... gca peak = 0.10426 (32) mri peak = 0.12812 (31) not using caudate to estimate GM means setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 1.23 x + 0 setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.33 x + 0 Fourth_Ventricle (15): linear fit = 1.00 x + 0.0 (1020 voxels, overlap=0.399) estimating mean gm scale to be 1.20 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.18 x + 0.0 24 transforms computed 0000: dt=0.000000, rms=0.735 (1.447%), neg=0, invalid=1511, LIN 0001: dt=0.000000, rms=0.728 (0.866%), neg=0, invalid=1511, LIN 0002: dt=0.000000, rms=0.726 (0.358%), neg=0, invalid=1511, LIN rms increased - undoing step... 0003: dt=0.000000, rms=0.725 (-0.005%), neg=0, invalid=1511, LIN rms increased - undoing step... 0005: dt=0.000000, rms=0.725 (-0.063%), neg=0, invalid=1511, LIN rms increased - undoing step... 0007: dt=0.000000, rms=0.724 (-0.241%), neg=0, invalid=1511, LIN rms increased - undoing step... 0009: dt=0.000000, rms=0.724 (-0.241%), neg=0, invalid=1511, LIN rms increased - undoing step... 0011: dt=0.000000, rms=0.723 (-0.267%), neg=0, invalid=1511, LIN rms increased - undoing step... 0013: dt=0.000000, rms=0.723 (-0.271%), neg=0, invalid=1511, LIN rms increased - undoing step... 0015: dt=0.000000, rms=0.723 (-0.280%), neg=0, invalid=1511, LIN rms increased - undoing step... 0017: dt=0.000000, rms=0.723 (-0.279%), neg=0, invalid=1511, LIN label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.720, neg=0, invalid=1511 0020: dt=216.726087, rms=0.671 (6.795%), neg=0, invalid=1511 0021: dt=153.403277, rms=0.653 (2.584%), neg=0, invalid=1511 0022: dt=199.377710, rms=0.645 (1.304%), neg=0, invalid=1511 0023: dt=141.398197, rms=0.640 (0.795%), neg=0, invalid=1511 0024: dt=221.952003, rms=0.635 (0.774%), neg=0, invalid=1511 0025: dt=120.120189, rms=0.632 (0.380%), neg=0, invalid=1511 0026: dt=517.888008, rms=0.627 (0.808%), neg=0, invalid=1511 0027: dt=87.443621, rms=0.624 (0.473%), neg=0, invalid=1511 0028: dt=2071.552031, rms=0.616 (1.395%), neg=0, invalid=1511 0029: dt=116.849928, rms=0.612 (0.587%), neg=0, invalid=1511 0030: dt=129.472002, rms=0.611 (0.105%), neg=0, invalid=1511 0031: dt=517.888008, rms=0.610 (0.185%), neg=0, invalid=1511 0032: dt=85.507087, rms=0.609 (0.138%), neg=0, invalid=1511 0033: dt=2071.552031, rms=0.605 (0.647%), neg=0, invalid=1511 0034: dt=92.480001, rms=0.605 (0.077%), neg=0, invalid=1511 0035: dt=517.888008, rms=0.604 (0.166%), neg=0, invalid=1511 0036: dt=129.472002, rms=0.604 (0.045%), neg=0, invalid=1511 0037: dt=129.472002, rms=0.603 (0.036%), neg=0, invalid=1511 0038: dt=129.472002, rms=0.603 (0.061%), neg=0, invalid=1511 0039: dt=129.472002, rms=0.603 (0.080%), neg=0, invalid=1511 0040: dt=129.472002, rms=0.602 (0.099%), neg=0, invalid=1511 0041: dt=129.472002, rms=0.601 (0.122%), neg=0, invalid=1511 0042: dt=129.472002, rms=0.600 (0.122%), neg=0, invalid=1511 0043: dt=129.472002, rms=0.600 (0.145%), neg=0, invalid=1511 0044: dt=129.472002, rms=0.599 (0.138%), neg=0, invalid=1511 0045: dt=129.472002, rms=0.598 (0.119%), neg=0, invalid=1511 0046: dt=129.472002, rms=0.597 (0.105%), neg=0, invalid=1511 0047: dt=129.472002, rms=0.597 (0.134%), neg=0, invalid=1511 0048: dt=129.472002, rms=0.596 (0.141%), neg=0, invalid=1511 0049: dt=129.472002, rms=0.595 (0.143%), neg=0, invalid=1511 0050: dt=129.472002, rms=0.594 (0.125%), neg=0, invalid=1511 0051: dt=129.472002, rms=0.594 (0.104%), neg=0, invalid=1511 0052: dt=129.472002, rms=0.593 (0.098%), neg=0, invalid=1511 0053: dt=129.472002, rms=0.592 (0.124%), neg=0, invalid=1511 0054: dt=129.472002, rms=0.592 (0.115%), neg=0, invalid=1511 0055: dt=129.472002, rms=0.591 (0.071%), neg=0, invalid=1511 0056: dt=129.472002, rms=0.591 (0.070%), neg=0, invalid=1511 0057: dt=129.472002, rms=0.590 (0.080%), neg=0, invalid=1511 0058: dt=129.472002, rms=0.590 (0.111%), neg=0, invalid=1511 0059: dt=129.472002, rms=0.589 (0.092%), neg=0, invalid=1511 0060: dt=129.472002, rms=0.589 (0.051%), neg=0, invalid=1511 0061: dt=129.472002, rms=0.588 (0.061%), neg=0, invalid=1511 0062: dt=129.472002, rms=0.588 (0.131%), neg=0, invalid=1511 0063: dt=129.472002, rms=0.587 (0.100%), neg=0, invalid=1511 0064: dt=129.472002, rms=0.587 (0.049%), neg=0, invalid=1511 0065: dt=129.472002, rms=0.587 (0.026%), neg=0, invalid=1511 0066: dt=129.472002, rms=0.586 (0.058%), neg=0, invalid=1511 0067: dt=129.472002, rms=0.586 (0.093%), neg=0, invalid=1511 0068: dt=129.472002, rms=0.585 (0.081%), neg=0, invalid=1511 0069: dt=129.472002, rms=0.585 (0.058%), neg=0, invalid=1511 0070: dt=129.472002, rms=0.585 (0.043%), neg=0, invalid=1511 0071: dt=129.472002, rms=0.584 (0.044%), neg=0, invalid=1511 0072: dt=129.472002, rms=0.584 (0.056%), neg=0, invalid=1511 0073: dt=129.472002, rms=0.584 (0.044%), neg=0, invalid=1511 0074: dt=129.472002, rms=0.584 (0.042%), neg=0, invalid=1511 0075: dt=129.472002, rms=0.583 (0.072%), neg=0, invalid=1511 0076: dt=129.472002, rms=0.583 (0.044%), neg=0, invalid=1511 0077: dt=129.472002, rms=0.583 (0.025%), neg=0, invalid=1511 0078: dt=129.472002, rms=0.583 (0.017%), neg=0, invalid=1511 0079: dt=129.472002, rms=0.582 (0.057%), neg=0, invalid=1511 0080: dt=129.472002, rms=0.582 (0.066%), neg=0, invalid=1511 0081: dt=129.472002, rms=0.582 (0.041%), neg=0, invalid=1511 0082: dt=129.472002, rms=0.582 (-0.004%), neg=0, invalid=1511 0083: dt=0.000000, rms=0.582 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.582, neg=0, invalid=1511 0084: dt=369.920006, rms=0.580 (0.218%), neg=0, invalid=1511 0085: dt=73.984001, rms=0.580 (0.006%), neg=0, invalid=1511 0086: dt=73.984001, rms=0.580 (0.013%), neg=0, invalid=1511 0087: dt=73.984001, rms=0.580 (0.011%), neg=0, invalid=1511 0088: dt=73.984001, rms=0.580 (0.019%), neg=0, invalid=1511 0089: dt=73.984001, rms=0.580 (0.028%), neg=0, invalid=1511 0090: dt=73.984001, rms=0.580 (0.048%), neg=0, invalid=1511 0091: dt=73.984001, rms=0.579 (0.047%), neg=0, invalid=1511 0092: dt=73.984001, rms=0.579 (0.038%), neg=0, invalid=1511 0093: dt=73.984001, rms=0.579 (0.029%), neg=0, invalid=1511 0094: dt=73.984001, rms=0.579 (0.032%), neg=0, invalid=1511 0095: dt=73.984001, rms=0.579 (0.040%), neg=0, invalid=1511 0096: dt=73.984001, rms=0.578 (0.028%), neg=0, invalid=1511 0097: dt=73.984001, rms=0.578 (0.020%), neg=0, invalid=1511 0098: dt=73.984001, rms=0.578 (0.022%), neg=0, invalid=1511 0099: dt=73.984001, rms=0.578 (0.039%), neg=0, invalid=1511 0100: dt=73.984001, rms=0.578 (0.038%), neg=0, invalid=1511 0101: dt=73.984001, rms=0.578 (0.026%), neg=0, invalid=1511 0102: dt=73.984001, rms=0.577 (0.026%), neg=0, invalid=1511 0103: dt=73.984001, rms=0.577 (0.023%), neg=0, invalid=1511 0104: dt=73.984001, rms=0.577 (0.018%), neg=0, invalid=1511 0105: dt=517.888008, rms=0.577 (0.039%), neg=0, invalid=1511 0106: dt=0.000000, rms=0.577 (-0.001%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.579, neg=0, invalid=1511 0107: dt=111.282571, rms=0.577 (0.389%), neg=0, invalid=1511 0108: dt=215.193044, rms=0.569 (1.306%), neg=0, invalid=1511 0109: dt=35.055124, rms=0.568 (0.321%), neg=0, invalid=1511 0110: dt=49.053035, rms=0.567 (0.103%), neg=0, invalid=1511 0111: dt=331.776005, rms=0.563 (0.702%), neg=0, invalid=1511 0112: dt=69.898007, rms=0.559 (0.678%), neg=0, invalid=1511 0113: dt=25.128029, rms=0.559 (0.046%), neg=0, invalid=1511 0114: dt=25.128029, rms=0.559 (0.059%), neg=0, invalid=1511 0115: dt=25.128029, rms=0.558 (0.110%), neg=0, invalid=1511 0116: dt=25.128029, rms=0.557 (0.175%), neg=0, invalid=1511 0117: dt=25.128029, rms=0.556 (0.220%), neg=0, invalid=1511 0118: dt=25.128029, rms=0.554 (0.247%), neg=0, invalid=1511 0119: dt=25.128029, rms=0.553 (0.246%), neg=0, invalid=1511 0120: dt=25.128029, rms=0.552 (0.256%), neg=0, invalid=1511 0121: dt=25.128029, rms=0.550 (0.265%), neg=0, invalid=1511 0122: dt=25.128029, rms=0.549 (0.263%), neg=0, invalid=1511 0123: dt=25.128029, rms=0.547 (0.254%), neg=0, invalid=1511 0124: dt=25.128029, rms=0.546 (0.240%), neg=0, invalid=1511 0125: dt=25.128029, rms=0.545 (0.229%), neg=0, invalid=1511 0126: dt=25.128029, rms=0.544 (0.230%), neg=0, invalid=1511 0127: dt=25.128029, rms=0.542 (0.235%), neg=0, invalid=1511 0128: dt=25.128029, rms=0.541 (0.213%), neg=0, invalid=1511 0129: dt=25.128029, rms=0.540 (0.200%), neg=0, invalid=1511 0130: dt=25.128029, rms=0.539 (0.192%), neg=0, invalid=1511 0131: dt=25.128029, rms=0.538 (0.186%), neg=0, invalid=1511 0132: dt=25.128029, rms=0.537 (0.177%), neg=0, invalid=1511 0133: dt=25.128029, rms=0.536 (0.154%), neg=0, invalid=1511 0134: dt=25.128029, rms=0.535 (0.143%), neg=0, invalid=1511 0135: dt=25.128029, rms=0.535 (0.140%), neg=0, invalid=1511 0136: dt=25.128029, rms=0.534 (0.137%), neg=0, invalid=1511 0137: dt=25.128029, rms=0.533 (0.132%), neg=0, invalid=1511 0138: dt=25.128029, rms=0.533 (0.122%), neg=0, invalid=1511 0139: dt=25.128029, rms=0.532 (0.114%), neg=0, invalid=1511 0140: dt=25.128029, rms=0.531 (0.114%), neg=0, invalid=1511 0141: dt=25.128029, rms=0.531 (0.120%), neg=0, invalid=1511 0142: dt=25.128029, rms=0.530 (0.123%), neg=0, invalid=1511 0143: dt=25.128029, rms=0.530 (0.113%), neg=0, invalid=1511 0144: dt=25.128029, rms=0.529 (0.094%), neg=0, invalid=1511 0145: dt=25.128029, rms=0.529 (0.082%), neg=0, invalid=1511 0146: dt=25.128029, rms=0.528 (0.077%), neg=0, invalid=1511 0147: dt=25.128029, rms=0.528 (0.080%), neg=0, invalid=1511 0148: dt=25.128029, rms=0.527 (0.088%), neg=0, invalid=1511 0149: dt=25.128029, rms=0.527 (0.083%), neg=0, invalid=1511 0150: dt=25.128029, rms=0.526 (0.076%), neg=0, invalid=1511 0151: dt=25.128029, rms=0.526 (0.071%), neg=0, invalid=1511 0152: dt=25.128029, rms=0.526 (0.071%), neg=0, invalid=1511 0153: dt=25.128029, rms=0.525 (0.073%), neg=0, invalid=1511 0154: dt=25.128029, rms=0.525 (0.068%), neg=0, invalid=1511 0155: dt=25.128029, rms=0.525 (0.067%), neg=0, invalid=1511 0156: dt=25.128029, rms=0.524 (0.062%), neg=0, invalid=1511 0157: dt=25.128029, rms=0.524 (0.064%), neg=0, invalid=1511 0158: dt=25.128029, rms=0.524 (0.059%), neg=0, invalid=1511 0159: dt=25.128029, rms=0.523 (0.054%), neg=0, invalid=1511 0160: dt=25.128029, rms=0.523 (0.052%), neg=0, invalid=1511 0161: dt=25.128029, rms=0.523 (0.056%), neg=0, invalid=1511 0162: dt=25.128029, rms=0.523 (0.052%), neg=0, invalid=1511 0163: dt=25.128029, rms=0.522 (0.050%), neg=0, invalid=1511 0164: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0165: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0166: dt=25.128029, rms=0.522 (0.048%), neg=0, invalid=1511 0167: dt=25.128029, rms=0.521 (0.044%), neg=0, invalid=1511 0168: dt=25.128029, rms=0.521 (0.043%), neg=0, invalid=1511 0169: dt=25.128029, rms=0.521 (0.044%), neg=0, invalid=1511 0170: dt=25.128029, rms=0.521 (0.038%), neg=0, invalid=1511 0171: dt=25.128029, rms=0.520 (0.036%), neg=0, invalid=1511 0172: dt=25.128029, rms=0.520 (0.038%), neg=0, invalid=1511 0173: dt=25.128029, rms=0.520 (0.040%), neg=0, invalid=1511 0174: dt=25.128029, rms=0.520 (0.038%), neg=0, invalid=1511 0175: dt=25.128029, rms=0.520 (0.032%), neg=0, invalid=1511 0176: dt=25.128029, rms=0.520 (0.031%), neg=0, invalid=1511 0177: dt=25.128029, rms=0.519 (0.036%), neg=0, invalid=1511 0178: dt=25.128029, rms=0.519 (0.037%), neg=0, invalid=1511 0179: dt=25.128029, rms=0.519 (0.038%), neg=0, invalid=1511 0180: dt=25.128029, rms=0.519 (0.036%), neg=0, invalid=1511 0181: dt=25.128029, rms=0.519 (0.025%), neg=0, invalid=1511 0182: dt=25.128029, rms=0.518 (0.023%), neg=0, invalid=1511 0183: dt=25.128029, rms=0.518 (0.024%), neg=0, invalid=1511 0184: dt=25.128029, rms=0.518 (0.032%), neg=0, invalid=1511 0185: dt=25.128029, rms=0.518 (0.043%), neg=0, invalid=1511 0186: dt=25.128029, rms=0.518 (0.041%), neg=0, invalid=1511 0187: dt=25.128029, rms=0.518 (0.030%), neg=0, invalid=1511 0188: dt=25.128029, rms=0.517 (0.022%), neg=0, invalid=1511 0189: dt=25.128029, rms=0.517 (0.015%), neg=0, invalid=1511 0190: dt=580.608009, rms=0.517 (0.079%), neg=0, invalid=1511 0191: dt=7.776000, rms=0.517 (-0.000%), neg=0, invalid=1511 0192: dt=7.776000, rms=0.517 (0.004%), neg=0, invalid=1511 0193: dt=7.776000, rms=0.517 (-0.010%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=1511 0194: dt=47.689071, rms=0.516 (0.131%), neg=0, invalid=1511 0195: dt=109.296352, rms=0.515 (0.283%), neg=0, invalid=1511 0196: dt=18.808524, rms=0.515 (0.039%), neg=0, invalid=1511 0197: dt=18.808524, rms=0.515 (0.005%), neg=0, invalid=1511 0198: dt=18.808524, rms=0.515 (-0.016%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.527, neg=0, invalid=1511 0199: dt=35.201863, rms=0.525 (0.386%), neg=0, invalid=1511 0200: dt=84.272825, rms=0.519 (1.215%), neg=0, invalid=1511 0201: dt=27.028692, rms=0.517 (0.320%), neg=0, invalid=1511 0202: dt=47.856551, rms=0.514 (0.625%), neg=0, invalid=1511 0203: dt=32.000000, rms=0.512 (0.423%), neg=0, invalid=1511 0204: dt=36.705510, rms=0.511 (0.247%), neg=0, invalid=1511 0205: dt=23.097180, rms=0.509 (0.333%), neg=0, invalid=1511 0206: dt=12.611658, rms=0.508 (0.077%), neg=0, invalid=1511 0207: dt=179.200003, rms=0.505 (0.729%), neg=0, invalid=1511 0208: dt=33.050655, rms=0.503 (0.390%), neg=0, invalid=1511 0209: dt=20.841661, rms=0.502 (0.150%), neg=0, invalid=1511 0210: dt=36.934922, rms=0.501 (0.182%), neg=0, invalid=1511 0211: dt=9.773344, rms=0.501 (0.037%), neg=0, invalid=1511 0212: dt=9.773344, rms=0.501 (0.038%), neg=0, invalid=1511 0213: dt=9.773344, rms=0.501 (0.032%), neg=0, invalid=1511 0214: dt=9.773344, rms=0.500 (0.076%), neg=0, invalid=1511 0215: dt=9.773344, rms=0.500 (0.129%), neg=0, invalid=1511 0216: dt=9.773344, rms=0.499 (0.127%), neg=0, invalid=1511 0217: dt=9.773344, rms=0.498 (0.121%), neg=0, invalid=1511 0218: dt=9.773344, rms=0.498 (0.101%), neg=0, invalid=1511 0219: dt=9.773344, rms=0.497 (0.120%), neg=0, invalid=1511 0220: dt=9.773344, rms=0.496 (0.161%), neg=0, invalid=1511 0221: dt=9.773344, rms=0.496 (0.169%), neg=0, invalid=1511 0222: dt=9.773344, rms=0.495 (0.144%), neg=0, invalid=1511 0223: dt=9.773344, rms=0.494 (0.111%), neg=0, invalid=1511 0224: dt=9.773344, rms=0.494 (0.111%), neg=0, invalid=1511 0225: dt=9.773344, rms=0.493 (0.134%), neg=0, invalid=1511 0226: dt=9.773344, rms=0.492 (0.141%), neg=0, invalid=1511 0227: dt=9.773344, rms=0.492 (0.116%), neg=0, invalid=1511 0228: dt=9.773344, rms=0.491 (0.089%), neg=0, invalid=1511 0229: dt=9.773344, rms=0.491 (0.081%), neg=0, invalid=1511 0230: dt=9.773344, rms=0.490 (0.097%), neg=0, invalid=1511 0231: dt=9.773344, rms=0.490 (0.101%), neg=0, invalid=1511 0232: dt=9.773344, rms=0.490 (0.079%), neg=0, invalid=1511 0233: dt=9.773344, rms=0.489 (0.063%), neg=0, invalid=1511 0234: dt=9.773344, rms=0.489 (0.053%), neg=0, invalid=1511 0235: dt=9.773344, rms=0.489 (0.064%), neg=0, invalid=1511 0236: dt=9.773344, rms=0.488 (0.072%), neg=0, invalid=1511 0237: dt=9.773344, rms=0.488 (0.059%), neg=0, invalid=1511 0238: dt=9.773344, rms=0.488 (0.043%), neg=0, invalid=1511 0239: dt=9.773344, rms=0.488 (0.038%), neg=0, invalid=1511 0240: dt=9.773344, rms=0.487 (0.048%), neg=0, invalid=1511 0241: dt=9.773344, rms=0.487 (0.053%), neg=0, invalid=1511 0242: dt=9.773344, rms=0.487 (0.043%), neg=0, invalid=1511 0243: dt=9.773344, rms=0.487 (0.030%), neg=0, invalid=1511 0244: dt=9.773344, rms=0.487 (0.031%), neg=0, invalid=1511 0245: dt=9.773344, rms=0.486 (0.044%), neg=0, invalid=1511 0246: dt=9.773344, rms=0.486 (0.053%), neg=0, invalid=1511 0247: dt=9.773344, rms=0.486 (0.032%), neg=0, invalid=1511 0248: dt=9.773344, rms=0.486 (0.024%), neg=0, invalid=1511 0249: dt=9.773344, rms=0.486 (0.022%), neg=0, invalid=1511 0250: dt=102.400002, rms=0.486 (0.049%), neg=0, invalid=1511 0251: dt=1.600000, rms=0.486 (-0.008%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.486, neg=0, invalid=1511 0252: dt=15.569267, rms=0.485 (0.141%), neg=0, invalid=1511 0253: dt=24.738315, rms=0.484 (0.222%), neg=0, invalid=1511 0254: dt=6.809498, rms=0.484 (0.031%), neg=0, invalid=1511 0255: dt=6.809498, rms=0.484 (0.019%), neg=0, invalid=1511 0256: dt=6.809498, rms=0.484 (0.017%), neg=0, invalid=1511 0257: dt=6.809498, rms=0.483 (0.049%), neg=0, invalid=1511 0258: dt=6.809498, rms=0.483 (0.071%), neg=0, invalid=1511 0259: dt=6.809498, rms=0.483 (0.052%), neg=0, invalid=1511 0260: dt=6.809498, rms=0.483 (0.022%), neg=0, invalid=1511 0261: dt=6.809498, rms=0.483 (0.009%), neg=0, invalid=1511 0262: dt=44.800001, rms=0.482 (0.039%), neg=0, invalid=1511 0263: dt=2.800000, rms=0.482 (-0.001%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0264: dt=0.000000, rms=0.510 (0.000%), neg=0, invalid=1511 0265: dt=0.150000, rms=0.510 (-0.008%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0266: dt=0.000000, rms=0.510 (-0.000%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.563, neg=0, invalid=1511 0267: dt=2.168286, rms=0.553 (1.795%), neg=0, invalid=1511 0268: dt=1.170096, rms=0.553 (0.134%), neg=0, invalid=1511 0269: dt=0.384000, rms=0.553 (0.009%), neg=0, invalid=1511 0270: dt=0.384000, rms=0.553 (-0.002%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.553, neg=0, invalid=1511 0271: dt=1.883680, rms=0.551 (0.227%), neg=0, invalid=1511 0272: dt=0.448000, rms=0.551 (0.014%), neg=0, invalid=1511 0273: dt=0.448000, rms=0.551 (0.006%), neg=0, invalid=1511 0274: dt=0.448000, rms=0.551 (-0.013%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=1511 0275: dt=0.448000, rms=0.496 (2.606%), neg=0, invalid=1511 0276: dt=1.536000, rms=0.487 (1.924%), neg=0, invalid=1511 0277: dt=0.384000, rms=0.487 (0.076%), neg=0, invalid=1511 0278: dt=0.000000, rms=0.487 (0.007%), neg=0, invalid=1511 0279: dt=0.050000, rms=0.487 (-0.001%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.487, neg=0, invalid=1511 0280: dt=0.448000, rms=0.483 (0.634%), neg=0, invalid=1511 0281: dt=0.448000, rms=0.483 (0.069%), neg=0, invalid=1511 0282: dt=0.448000, rms=0.483 (0.062%), neg=0, invalid=1511 0283: dt=0.448000, rms=0.483 (0.052%), neg=0, invalid=1511 0284: dt=0.448000, rms=0.482 (0.053%), neg=0, invalid=1511 0285: dt=0.448000, rms=0.482 (0.048%), neg=0, invalid=1511 0286: dt=0.448000, rms=0.482 (0.044%), neg=0, invalid=1511 0287: dt=0.448000, rms=0.481 (0.080%), neg=0, invalid=1511 0288: dt=0.448000, rms=0.481 (0.107%), neg=0, invalid=1511 0289: dt=0.448000, rms=0.480 (0.119%), neg=0, invalid=1511 0290: dt=0.448000, rms=0.480 (0.120%), neg=0, invalid=1511 0291: dt=0.448000, rms=0.480 (0.011%), neg=0, invalid=1511 0292: dt=0.448000, rms=0.480 (0.013%), neg=0, invalid=1511 0293: dt=0.448000, rms=0.480 (0.027%), neg=0, invalid=1511 0294: dt=0.448000, rms=0.479 (0.029%), neg=0, invalid=1511 0295: dt=0.056000, rms=0.479 (0.002%), neg=0, invalid=1511 0296: dt=0.056000, rms=0.479 (0.003%), neg=0, invalid=1511 0297: dt=0.056000, rms=0.479 (0.001%), neg=0, invalid=1511 0298: dt=0.448000, rms=0.479 (0.009%), neg=0, invalid=1511 0299: dt=0.001750, rms=0.479 (-0.001%), neg=0, invalid=1511 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.01 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.477, neg=0, invalid=1511 0300: dt=129.472002, rms=0.477 (0.030%), neg=0, invalid=1511 0301: dt=129.472002, rms=0.477 (0.057%), neg=0, invalid=1511 0302: dt=32.368000, rms=0.477 (0.009%), neg=0, invalid=1511 0303: dt=32.368000, rms=0.476 (0.008%), neg=0, invalid=1511 0304: dt=16.184000, rms=0.476 (0.004%), neg=0, invalid=1511 0305: dt=4.046000, rms=0.476 (0.001%), neg=0, invalid=1511 0306: dt=0.505750, rms=0.476 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.476, neg=0, invalid=1511 0307: dt=129.472002, rms=0.476 (0.169%), neg=0, invalid=1511 0308: dt=295.936004, rms=0.475 (0.056%), neg=0, invalid=1511 0309: dt=129.472002, rms=0.475 (0.060%), neg=0, invalid=1511 0310: dt=92.480001, rms=0.475 (0.019%), neg=0, invalid=1511 0311: dt=92.480001, rms=0.475 (0.015%), neg=0, invalid=1511 0312: dt=92.480001, rms=0.475 (0.024%), neg=0, invalid=1511 0313: dt=92.480001, rms=0.475 (0.035%), neg=0, invalid=1511 0314: dt=92.480001, rms=0.474 (0.037%), neg=0, invalid=1511 0315: dt=92.480001, rms=0.474 (0.039%), neg=0, invalid=1511 0316: dt=92.480001, rms=0.474 (0.037%), neg=0, invalid=1511 0317: dt=92.480001, rms=0.474 (0.035%), neg=0, invalid=1511 0318: dt=92.480001, rms=0.474 (0.034%), neg=0, invalid=1511 0319: dt=92.480001, rms=0.474 (0.030%), neg=0, invalid=1511 0320: dt=92.480001, rms=0.474 (0.027%), neg=0, invalid=1511 0321: dt=92.480001, rms=0.473 (0.025%), neg=0, invalid=1511 0322: dt=92.480001, rms=0.473 (0.023%), neg=0, invalid=1511 0323: dt=295.936004, rms=0.473 (0.009%), neg=0, invalid=1511 0324: dt=295.936004, rms=0.473 (-0.031%), neg=0, invalid=1511 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0325: dt=36.288001, rms=0.473 (0.063%), neg=0, invalid=1511 0326: dt=14.141785, rms=0.473 (0.020%), neg=0, invalid=1511 0327: dt=7.070892, rms=0.473 (0.010%), neg=0, invalid=1511 0328: dt=1.767723, rms=0.473 (0.003%), neg=0, invalid=1511 0329: dt=0.220965, rms=0.473 (0.000%), neg=0, invalid=1511 0330: dt=0.101250, rms=0.473 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0331: dt=0.035438, rms=0.473 (0.000%), neg=0, invalid=1511 0332: dt=0.035438, rms=0.473 (0.000%), neg=0, invalid=1511 0333: dt=0.008859, rms=0.473 (0.000%), neg=0, invalid=1511 0334: dt=0.002215, rms=0.473 (0.000%), neg=0, invalid=1511 0335: dt=0.000017, rms=0.473 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0336: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.473, neg=0, invalid=1511 0337: dt=0.000000, rms=0.473 (0.000%), neg=0, invalid=1511 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=1511 0338: dt=4.032000, rms=0.467 (1.406%), neg=0, invalid=1511 0339: dt=4.032000, rms=0.463 (0.974%), neg=0, invalid=1511 0340: dt=11.520000, rms=0.454 (1.818%), neg=0, invalid=1511 0341: dt=1.008000, rms=0.454 (0.059%), neg=0, invalid=1511 0342: dt=2.880000, rms=0.453 (0.173%), neg=0, invalid=1511 0343: dt=4.032000, rms=0.452 (0.212%), neg=0, invalid=1511 0344: dt=1.008000, rms=0.452 (0.042%), neg=0, invalid=1511 0345: dt=1.008000, rms=0.452 (0.040%), neg=0, invalid=1511 0346: dt=1.008000, rms=0.451 (0.075%), neg=0, invalid=1511 0347: dt=1.008000, rms=0.451 (0.102%), neg=0, invalid=1511 0348: dt=1.008000, rms=0.450 (0.121%), neg=0, invalid=1511 0349: dt=1.008000, rms=0.450 (0.132%), neg=0, invalid=1511 0350: dt=1.008000, rms=0.449 (0.138%), neg=0, invalid=1511 0351: dt=1.008000, rms=0.449 (0.137%), neg=0, invalid=1511 0352: dt=1.008000, rms=0.448 (0.131%), neg=0, invalid=1511 0353: dt=1.008000, rms=0.447 (0.121%), neg=0, invalid=1511 0354: dt=1.008000, rms=0.447 (0.108%), neg=0, invalid=1511 0355: dt=1.008000, rms=0.447 (0.094%), neg=0, invalid=1511 0356: dt=1.008000, rms=0.446 (0.080%), neg=0, invalid=1511 0357: dt=1.008000, rms=0.446 (0.065%), neg=0, invalid=1511 0358: dt=1.008000, rms=0.446 (-0.006%), neg=0, invalid=1511 0359: dt=0.000000, rms=0.446 (-0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.446, neg=0, invalid=1511 0360: dt=4.032000, rms=0.445 (0.220%), neg=0, invalid=1511 0361: dt=4.032000, rms=0.444 (0.121%), neg=0, invalid=1511 0362: dt=13.824000, rms=0.444 (0.150%), neg=0, invalid=1511 0363: dt=4.032000, rms=0.444 (0.019%), neg=0, invalid=1511 0364: dt=4.032000, rms=0.444 (0.017%), neg=0, invalid=1511 0365: dt=4.032000, rms=0.443 (0.030%), neg=0, invalid=1511 0366: dt=4.032000, rms=0.443 (0.034%), neg=0, invalid=1511 0367: dt=4.032000, rms=0.443 (0.034%), neg=0, invalid=1511 0368: dt=4.032000, rms=0.443 (0.040%), neg=0, invalid=1511 0369: dt=4.032000, rms=0.443 (0.052%), neg=0, invalid=1511 0370: dt=4.032000, rms=0.442 (0.070%), neg=0, invalid=1511 0371: dt=4.032000, rms=0.442 (0.091%), neg=0, invalid=1511 0372: dt=4.032000, rms=0.442 (0.104%), neg=0, invalid=1511 0373: dt=4.032000, rms=0.441 (0.111%), neg=0, invalid=1511 0374: dt=4.032000, rms=0.441 (0.110%), neg=0, invalid=1511 0375: dt=4.032000, rms=0.440 (0.102%), neg=0, invalid=1511 0376: dt=4.032000, rms=0.440 (0.088%), neg=0, invalid=1511 0377: dt=4.032000, rms=0.439 (0.073%), neg=0, invalid=1511 0378: dt=4.032000, rms=0.439 (0.058%), neg=0, invalid=1511 0379: dt=4.032000, rms=0.439 (0.044%), neg=0, invalid=1511 0380: dt=4.032000, rms=0.439 (0.034%), neg=0, invalid=1511 0381: dt=4.032000, rms=0.439 (0.027%), neg=0, invalid=1511 0382: dt=4.032000, rms=0.439 (0.021%), neg=0, invalid=1511 0383: dt=4.032000, rms=0.439 (0.018%), neg=0, invalid=1511 0384: dt=16.128000, rms=0.438 (0.010%), neg=0, invalid=1511 0385: dt=16.128000, rms=0.438 (0.000%), neg=0, invalid=1511 0386: dt=16.128000, rms=0.438 (-0.005%), neg=0, invalid=1511 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.445, neg=0, invalid=1511 0387: dt=0.000000, rms=0.445 (-0.000%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.445, neg=0, invalid=1511 0388: dt=0.000000, rms=0.445 (0.000%), neg=0, invalid=1511 0389: dt=0.100000, rms=0.445 (-0.069%), neg=0, invalid=1511 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.434, neg=0, invalid=1511 0390: dt=0.112000, rms=0.432 (0.533%), neg=0, invalid=1511 0391: dt=0.112000, rms=0.430 (0.403%), neg=0, invalid=1511 0392: dt=0.028000, rms=0.430 (0.078%), neg=0, invalid=1511 0393: dt=0.112000, rms=0.428 (0.291%), neg=0, invalid=1511 0394: dt=0.112000, rms=0.427 (0.226%), neg=0, invalid=1511 0395: dt=0.112000, rms=0.427 (0.178%), neg=0, invalid=1511 0396: dt=0.028000, rms=0.427 (0.035%), neg=0, invalid=1511 0397: dt=0.028000, rms=0.426 (0.034%), neg=0, invalid=1511 0398: dt=0.028000, rms=0.426 (0.062%), neg=0, invalid=1511 0399: dt=0.028000, rms=0.426 (0.085%), neg=0, invalid=1511 0400: dt=0.028000, rms=0.425 (0.100%), neg=0, invalid=1511 0401: dt=0.028000, rms=0.425 (0.110%), neg=0, invalid=1511 0402: dt=0.028000, rms=0.424 (0.112%), neg=0, invalid=1511 0403: dt=0.014000, rms=0.424 (0.005%), neg=0, invalid=1511 0404: dt=0.014000, rms=0.424 (0.005%), neg=0, invalid=1511 0405: dt=0.028000, rms=0.424 (0.010%), neg=0, invalid=1511 0406: dt=0.028000, rms=0.424 (0.010%), neg=0, invalid=1511 0407: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 0408: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 0409: dt=0.007000, rms=0.424 (0.005%), neg=0, invalid=1511 0410: dt=0.007000, rms=0.424 (0.006%), neg=0, invalid=1511 0411: dt=0.007000, rms=0.424 (0.008%), neg=0, invalid=1511 0412: dt=0.007000, rms=0.424 (0.009%), neg=0, invalid=1511 0413: dt=0.007000, rms=0.424 (0.011%), neg=0, invalid=1511 0414: dt=0.007000, rms=0.424 (0.012%), neg=0, invalid=1511 0415: dt=0.007000, rms=0.424 (0.012%), neg=0, invalid=1511 0416: dt=0.007000, rms=0.424 (0.013%), neg=0, invalid=1511 0417: dt=0.007000, rms=0.424 (0.013%), neg=0, invalid=1511 0418: dt=0.007000, rms=0.424 (0.002%), neg=0, invalid=1511 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=1511 0419: dt=0.024000, rms=0.424 (0.044%), neg=0, invalid=1511 0420: dt=0.028000, rms=0.423 (0.049%), neg=0, invalid=1511 0421: dt=0.028000, rms=0.423 (0.045%), neg=0, invalid=1511 0422: dt=0.028000, rms=0.423 (0.042%), neg=0, invalid=1511 0423: dt=0.028000, rms=0.423 (0.077%), neg=0, invalid=1511 0424: dt=0.028000, rms=0.423 (0.035%), neg=0, invalid=1511 0425: dt=0.028000, rms=0.422 (0.063%), neg=0, invalid=1511 0426: dt=0.028000, rms=0.422 (0.084%), neg=0, invalid=1511 0427: dt=0.028000, rms=0.422 (0.097%), neg=0, invalid=1511 0428: dt=0.028000, rms=0.421 (0.018%), neg=0, invalid=1511 0429: dt=0.028000, rms=0.421 (0.032%), neg=0, invalid=1511 0430: dt=0.028000, rms=0.421 (0.044%), neg=0, invalid=1511 0431: dt=0.028000, rms=0.421 (0.013%), neg=0, invalid=1511 0432: dt=0.028000, rms=0.421 (0.024%), neg=0, invalid=1511 0433: dt=0.028000, rms=0.421 (0.033%), neg=0, invalid=1511 0434: dt=0.028000, rms=0.421 (0.009%), neg=0, invalid=1511 0435: dt=0.028000, rms=0.421 (0.018%), neg=0, invalid=1511 0436: dt=0.028000, rms=0.421 (0.024%), neg=0, invalid=1511 0437: dt=0.028000, rms=0.421 (0.029%), neg=0, invalid=1511 0438: dt=0.014000, rms=0.421 (0.003%), neg=0, invalid=1511 0439: dt=0.014000, rms=0.421 (0.006%), neg=0, invalid=1511 0440: dt=0.014000, rms=0.420 (0.003%), neg=0, invalid=1511 0441: dt=0.112000, rms=0.420 (0.023%), neg=0, invalid=1511 0442: dt=0.096000, rms=0.420 (0.016%), neg=0, invalid=1511 0443: dt=0.048000, rms=0.420 (0.007%), neg=0, invalid=1511 0444: dt=0.024000, rms=0.420 (0.00Segmentation fault ERROR: mri_ca_register with non-zero status Linux ConnorLabUbuntu 2.6.15-27-386 #1 PREEMPT Fri Dec 8 17:51:56 UTC 2006 i686 GNU/Linux recon-all exited with ERRORS at Fri Feb 9 01:43:48 CST 2007