Fri Jul 14 16:08:35 EDT 2006 /usr/local/freesurfer/subjects/E_062 /usr/local/freesurfer/bin//recon-all -i /root/Unflipped_Brains/E_062_nuc50.mnc -subjid E_062 -sd /usr/local/freesurfer/subjects -all subjid E_062 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer Linux dhcp-129-105-146-221.speech.northwestern.edu 2.4.22-10mdk #1 Thu Sep 18 12:30:58 CEST 2003 i686 unknown unknown GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 1000000 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 4083 ######################################## program versions used $Id: recon-all,v 1.17.2.4 2006/05/02 18:28:49 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: 06/07/14-20:08:35-GMT CVS: $Id: mri_convert.c,v 1.121 2006/02/22 05:39:36 greve Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk 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: 06/07/14-20:08:35-GMT CVS: $Id: mri_normalize.c,v 1.44.2.1 2006/04/12 02:02:57 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_watershed.cpp,v 1.48 2006/02/27 16:57:57 segonne Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_segment.c,v 1.28.2.1 2006/04/12 02:02:58 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_fill.c,v 1.101 2006/02/22 23:05:06 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_tessellate.c,v 1.27.2.1 2006/05/02 21:41:01 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_smooth.c,v 1.13.2.1 2006/05/02 21:41:01 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_inflate.c,v 1.30.2.1 2006/05/02 21:41:01 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_sphere.c,v 1.38 2006/02/08 00:17:40 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_euler_number.c,v 1.4 2003/09/05 04:45:41 kteich Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_make_surfaces.c,v 1.70.2.1 2006/04/12 02:02:59 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mris_register.c,v 1.32 2005/12/07 14:22:57 fischl Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mrisp_paint.c,v 1.6 2005/02/14 04:30:19 segonne Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_label2label.c,v 1.23 2006/02/19 17:55:08 greve Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_em_register.c,v 1.52 2006/01/11 21:01:40 greve Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_ca_normalize.c,v 1.31 2005/08/15 14:14:22 fischl Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_ca_register.c,v 1.48 2006/02/23 15:53:27 xhan Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk CompilerName: GCC CompilerVersion: 30200 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 06/07/14-20:08:36-GMT CVS: $Id: mri_ca_label.c,v 1.68 2006/01/22 04:26:26 nicks Exp $ User: root Machine: dhcp-129-105-146-221.speech.northwestern.edu Platform: Linux PlatformVersion: 2.4.22-10mdk 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 ####################################### /usr/local/freesurfer/subjects/E_062 mri_convert /root/Unflipped_Brains/E_062_nuc50.mnc /usr/local/freesurfer/subjects/E_062/mri/orig/001.mgz mri_convert /root/Unflipped_Brains/E_062_nuc50.mnc /usr/local/freesurfer/subjects/E_062/mri/orig/001.mgz reading from /root/Unflipped_Brains/E_062_nuc50.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /usr/local/freesurfer/subjects/E_062/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Jul 14 16:08:42 EDT 2006 Found 1 runs /usr/local/freesurfer/subjects/E_062/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/E_062/mri/orig/001.mgz /usr/local/freesurfer/subjects/E_062/mri/rawavg.mgz /usr/local/freesurfer/subjects/E_062 mri_convert /usr/local/freesurfer/subjects/E_062/mri/rawavg.mgz /usr/local/freesurfer/subjects/E_062/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/E_062/mri/rawavg.mgz /usr/local/freesurfer/subjects/E_062/mri/orig.mgz --conform reading from /usr/local/freesurfer/subjects/E_062/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (181, 217, 181) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from 4 to 0 (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/E_062/mri/orig.mgz... mri_add_xform_to_header -c /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/E_062/mri/orig.mgz /usr/local/freesurfer/subjects/E_062/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Fri Jul 14 16:09:04 EDT 2006 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /usr/local/freesurfer/subjects/E_062/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 2005/12/08 01:27:21 greve Exp $ Linux dhcp-129-105-146-221.speech.northwestern.edu 2.4.22-10mdk #1 Thu Sep 18 12:30:58 CEST 2003 i686 unknown unknown GNU/Linux Fri Jul 14 16:09:04 EDT 2006 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.2979 /usr/local/freesurfer/subjects/E_062/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2979/nu0.mnc mri_convert orig.mgz ./tmp.mri_nu_correct.mni.2979/nu0.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from orig.mgz... Talairach transform /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to ./tmp.mri_nu_correct.mni.2979/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Jul 14 16:09:13 EDT 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.2979/nu0.mnc ./tmp.mri_nu_correct.mni.2979/nu1.mnc [root@dhcp-129-105-146-221.speech.northwestern.edu:/usr/local/freesurfer/subjects/E_062/mri/] [2006-07-14 16:09:14] 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 /root/tmp/nu_correct_3023/ ./tmp.mri_nu_correct.mni.2979/nu0.mnc ./tmp.mri_nu_correct.mni.2979/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() Number of iterations: 32 CV of field change: 0.000914433 [root@dhcp-129-105-146-221.speech.northwestern.edu:/usr/local/freesurfer/subjects/E_062/mri/] [2006-07-14 16:10:27] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2979/nu0.mnc /root/tmp/nu_correct_3023//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 Jul 14 16:10:35 EDT 2006 nu_correct -clobber ./tmp.mri_nu_correct.mni.2979/nu1.mnc ./tmp.mri_nu_correct.mni.2979/nu2.mnc [root@dhcp-129-105-146-221.speech.northwestern.edu:/usr/local/freesurfer/subjects/E_062/mri/] [2006-07-14 16:10:35] 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 /root/tmp/nu_correct_3452/ ./tmp.mri_nu_correct.mni.2979/nu1.mnc ./tmp.mri_nu_correct.mni.2979/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() Number of iterations: 10 CV of field change: 0.00096981 [root@dhcp-129-105-146-221.speech.northwestern.edu:/usr/local/freesurfer/subjects/E_062/mri/] [2006-07-14 16:11:01] running: /usr/local/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.2979/nu1.mnc /root/tmp/nu_correct_3452//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.2979/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.2979/nu2.mnc nu.mgz --like orig.mgz Can't find the talairach xform '/usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from ./tmp.mri_nu_correct.mni.2979/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz Talairach transform /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm writing to nu.mgz... Fri Jul 14 16:11:26 EDT 2006 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Fri Jul 14 16:11:26 EDT 2006 /usr/local/freesurfer/subjects/E_062/mri talairach --i nu.mgz --xfm transforms/talairach.auto.xfm /usr/local/freesurfer/subjects/E_062/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 dhcp-129-105-146-221.speech.northwestern.edu 2.4.22-10mdk #1 Thu Sep 18 12:30:58 CEST 2003 i686 unknown unknown GNU/Linux Fri Jul 14 16:11:26 EDT 2006 tmpdir is transforms/tmp.talairach.3645 /usr/local/freesurfer/subjects/E_062/mri mri_convert nu.mgz transforms/tmp.talairach.3645/src.mnc mri_convert nu.mgz transforms/tmp.talairach.3645/src.mnc Can't find the talairach xform '/usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm' Transform is not loaded into mri reading from nu.mgz... Talairach transform /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm does not exist ... Cannot load tal xfm file /usr/local/freesurfer/subjects/E_062/mri/transforms/talairach.xfm TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.3645/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3645/src.mnc transforms/talairach.auto.xfm Fri Jul 14 16:12:24 EDT 2006 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Intensity Normalization Fri Jul 14 16:12:25 EDT 2006 /usr/local/freesurfer/subjects/E_062/mri mri_normalize -g 1 nu.mgz T1.mgz WM removal version using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.970 -0.008 -0.000 0.889; 0.009 1.042 0.038 0.124; -0.000 -0.035 0.951 -1.019; 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 5 minutes and 40 seconds. white matter peak found at 110 gm peak at 76 (76), valley at 59 (59) csf peak at 12, setting threshold to 54 white matter peak found at 110 gm peak at 76 (76), valley at 59 (59) csf peak at 12, setting threshold to 54 #-------------------------------------------- #@# Skull Stripping Fri Jul 14 16:18:08 EDT 2006 /usr/local/freesurfer/subjects/E_062/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 : 432393 Find the largest 110-component... heap usage = 449940 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 419996 voxels first estimation of the COG coord: x=128 y=133 z=126 r=90 first estimation of the main basin volume: 3085278 voxels global maximum in x=105, y=116, z=82, Imax=255 CSF=16, 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= 2466019 voxels, voxel volume =1.000 = 2466019 mmm3 = 2466.019 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=136, z=124, r=10555 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=44, TRANSITION=47, GM_MIN=50, GM=77 after analyzing : CSF_MAX=44, TRANSITION=49, GM_MIN=50, GM=56 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...76 iterations *********************VALIDATION********************* No Rigid alignment: Atlas Mode Off before rotation: sse = 5.30, sigma = 7.59 after rotation: sse = 5.30, sigma = 7.59 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.80, its var is 7.15 before Erosion-Dilatation 8.49% of inacurate vertices after Erosion-Dilatation 8.88% of inacurate vertices 2.53% of 'positive' inacurate vertices 97.47% of 'negative' inacurate vertices THE SEGMENTATION IS PROBABLY NOT CORRECT ********************************************** ********************************************** If the final segmentation is not valid, try using the option '-atlas' ********************************************** ********************************************** Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...44 iterations mri_strip_skull: done peeling brain Brain Size = 2388920 voxels, voxel volume = 1.000 mm3 = 2388920 mmm3 = 2388.920 cm3 ****************************** Save...done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Jul 14 16:20:09 EDT 2006 /usr/local/freesurfer/subjects/E_062/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, -18.7, -19.9): log p = -12082.7 Result so far: scale 1.000: max_log_p=-11358.0, old_max_log_p =-12082.7 (thresh=-12070.6) 1.000 0.000 0.000 -2.841; 0.000 0.938 0.000 -10.171; 0.000 0.000 1.000 -19.886; 0.000 0.000 0.000 1.000; Result so far: scale 1.000: max_log_p=-11358.0, old_max_log_p =-11358.0 (thresh=-11346.6) 1.000 0.000 0.000 -2.841; 0.000 0.938 0.000 -10.171; 0.000 0.000 1.000 -19.886; 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 1.00000 0.00000 0.00000 -2.84091; 0.00000 0.93750 0.00000 -10.17134; 0.00000 0.00000 1.00000 -19.88636; 0.00000 0.00000 0.00000 1.00000; nsamples 2242 Quasinewton: input matrix 1.00000 0.00000 0.00000 -2.84091; 0.00000 0.93750 0.00000 -10.17134; 0.00000 0.00000 1.00000 -19.88636; 0.00000 0.00000 0.00000 1.00000; pass 2 through quasi-newton minimization... fp = 11344.117188, fret = 11344.760742, 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 1.00000 0.00000 0.00000 -2.84091; 0.00000 0.93750 0.00000 -10.17134; 0.00000 0.00000 1.00000 -19.88636; 0.00000 0.00000 0.00000 1.00000; nsamples 242283 Quasinewton: input matrix 1.00000 0.00000 0.00000 -2.84091; 0.00000 0.93750 0.00000 -10.17134; 0.00000 0.00000 1.00000 -19.88636; 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... fp = 1380621.125000, fret = 1380621.125000, ftol = 0.000000, EPS = 0.000000 freeing gibbs priors...done. bounding unknown intensity as < 16.0 or > 799.3 ************************************************ spacing=8, using 2242 sample points, tol=1.00e-05... ************************************************ Note: program considers input volume #1 as the most T1-like using real data threshold=28.0 using (104, 107, 130) as brain centroid... mean wm in atlas = 109, using box (85,89,107) --> (122, 125,152) to find MRI wm before smoothing, mri peak at 145 after smoothing, mri peak at 144, scaling input intensities by 0.756 scaling channel 0 by 0.756046 initial log_p = -50624.2 **************************************** 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) = 11358.0 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 003: -log(p) = 11344.1 after pass:transform: ( 1.00, -0.00, -0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( -0.00, -0.00, 1.00, -19.89) outof QuasiNewtonEMA: 005: -log(p) = 11344.1 tol 0.000010 Resulting transform: 1.000 0.000 0.000 -2.841; 0.000 0.938 0.000 -10.171; 0.000 0.000 1.000 -19.886; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -11358.0 (old=-50624.2) transform before final EM align: 1.000 0.000 0.000 -2.841; 0.000 0.938 0.000 -10.171; 0.000 0.000 1.000 -19.886; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 242283 samples. ************************************************** dfp_em_step_func: 004: -log(p) = 1390360.2 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 005: -log(p) = 1385577.1 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 006: -log(p) = 1384566.2 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 007: -log(p) = 1381929.6 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 008: -log(p) = 1380641.2 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) dfp_em_step_func: 009: -log(p) = 1380621.1 after pass:transform: ( 1.00, 0.00, 0.00, -2.84) ( 0.00, 0.94, 0.00, -10.17) ( 0.00, 0.00, 1.00, -19.89) outof QuasiNewtonEMA: 011: -log(p) = 1380621.1 tol 0.000000 final transform: 1.000 0.001 0.001 -2.841; 0.002 0.939 0.002 -10.171; 0.000 0.001 1.000 -19.886; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 6 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Fri Jul 14 16:26:59 EDT 2006 /usr/local/freesurfer/subjects/E_062/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 1.000 0.001 0.001 -2.841; 0.002 0.939 0.002 -10.171; 0.000 0.001 1.000 -19.886; 0.000 0.000 0.000 1.000; INFO: transform used reading input volume from nu.mgz... Note: program considers input volume #1 as the most T1-like using real data threshold=28.0 using (104, 107, 130) as brain centroid... mean wm in atlas = 109, using box (85,89,107) --> (122, 125,152) to find MRI wm before smoothing, mri peak at 145 after smoothing, mri peak at 144, scaling input intensities by 0.756 scaling channel 0 by 0.756046 using 242283 sample points... finding control points in Left_Cerebral_White_Matter.... found 38929 control points for structure... bounding box (129, 66, 46) --> (195, 191, 212) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 110.0 1019 of 4144 (24.6%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 38531 control points for structure... bounding box (65, 66, 46) --> (129, 191, 212) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 111.0 958 of 3930 (24.4%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3087 control points for structure... bounding box (131, 157, 68) --> (177, 202, 122) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 108.0 47 of 188 (25.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2900 control points for structure... bounding box (83, 159, 66) --> (129, 202, 122) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 113.0 32 of 140 (22.9%) samples deleted finding control points in Brain_Stem.... found 3414 control points for structure... bounding box (111, 147, 102) --> (145, 221, 134) Brain_Stem: limiting intensities to 92.0 --> 107.0 89 of 306 (29.1%) samples deleted using 8708 total control points for intensity normalization... bias field = 1.076 +- 0.069 35 of 6563 control points discarded writing normalized volume to norm.mgz... freeing GCA...done. normalization took 1 minutes and 25 seconds. #-------------------------------------- #@# CA Reg Fri Jul 14 16:28:25 EDT 2006 /usr/local/freesurfer/subjects/E_062/mri mri_ca_register -align -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 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 Right_Cerebral_White_Matter... source mean =75.5969, std = 18.3542 X:62-133; Y:63-196; Z:43-216 gca peak = 0.05652 (116) mri peak = 0.08991 (114) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (146096 voxels, overlap=0.499) aligning Left_Cerebral_White_Matter... source mean =75.5961, std = 18.1807 X:126-199; Y:63-196; Z:43-216 gca peak = 0.05682 (116) mri peak = 0.08799 (114) Left_Cerebral_White_Matter (2): linear fit = 0.98 x + 0.0 (155175 voxels, overlap=0.467) aligning Right_Hippocampus... source mean =79.7299, std = 22.1269 X:89-122; Y:139-182; Z:104-145 gca peak = 0.14805 (66) mri peak = 0.07237 (82) Right_Hippocampus (53): linear fit = 1.23 x + 0.0 (2979 voxels, overlap=0.042) aligning Left_Hippocampus... source mean =78.2475, std = 20.9419 X:137-170; Y:137-182; Z:100-145 gca peak = 0.17297 (66) mri peak = 0.06232 (82) Left_Hippocampus (17): linear fit = 1.17 x + 0.0 (2471 voxels, overlap=0.068) aligning Left_Cerebral_Cortex... gca peak = 0.05671 (68) mri peak = 0.02420 (79) uniform distribution in MR - rejecting arbitrary fit aligning Right_Cerebral_Cortex... gca peak = 0.06581 (70) mri peak = 0.02579 (79) uniform distribution in MR - rejecting arbitrary fit aligning Left_Lateral_Ventricle... source mean =68.3524, std = 36.4885 X:128-165; Y:114-155; Z:83-178 gca peak = 0.05153 (25) mri peak = 0.03004 (86) Left_Lateral_Ventricle (4): linear fit = 2.28 x + 0.0 (8950 voxels, overlap=0.000) aligning Right_Lateral_Ventricle... source mean =69.1343, std = 37.4888 X:94-133; Y:114-158; Z:73-178 gca peak = 0.07557 (30) mri peak = 0.03867 (28) Right_Lateral_Ventricle (43): linear fit = 3.40 x + 0.0 (5219 voxels, overlap=0.080) aligning Right_Caudate... source mean =84.1463, std = 27.9684 X:109-130; Y:117-161; Z:124-175 gca peak = 0.07786 (81) mri peak = 0.11837 (89) Right_Caudate (50): linear fit = 1.12 x + 0.0 (1990 voxels, overlap=0.227) aligning Left_Caudate... source mean =83.1499, std = 26.478 X:131-152; Y:115-163; Z:120-175 gca peak = 0.07814 (81) mri peak = 0.06472 (88) Left_Caudate (11): linear fit = 1.12 x + 0.0 (1281 voxels, overlap=0.445) aligning Left_Cerebellum_Cortex... source mean =56.3692, std = 19.6715 X:126-191; Y:144-221; Z:55-122 gca peak = 0.06033 (63) mri peak = 0.04497 (80) Left_Cerebellum_Cortex (8): linear fit = 1.30 x + 0.0 (34620 voxels, overlap=0.033) aligning Right_Cerebellum_Cortex... source mean =56.6483, std = 19.8383 X:70-133; Y:144-224; Z:55-122 gca peak = 0.05990 (64) mri peak = 0.04792 (84) Right_Cerebellum_Cortex (47): linear fit = 1.33 x + 0.0 (46775 voxels, overlap=0.038) aligning Left_Cerebellum_White_Matter... source mean =86.0754, std = 11.7824 X:128-181; Y:155-207; Z:65-126 gca peak = 0.09299 (92) mri peak = 0.11039 (100) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7528 voxels, overlap=0.244) aligning Right_Cerebellum_White_Matter... source mean =86.6104, std = 12.2125 X:80-133; Y:157-207; Z:63-126 gca peak = 0.08899 (93) mri peak = 0.12126 (101) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (5531 voxels, overlap=0.087) aligning Left_Amygdala... source mean =70.8501, std = 17.458 X:137-164; Y:158-184; Z:132-151 gca peak = 0.13911 (71) mri peak = 0.07186 (78) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (1604 voxels, overlap=0.174) aligning Right_Amygdala... source mean =71.7865, std = 17.8247 X:95-122; Y:158-184; Z:132-151 gca peak = 0.15703 (65) mri peak = 0.07542 (87) Right_Amygdala (54): linear fit = 1.27 x + 0.0 (1068 voxels, overlap=0.012) aligning Left_Thalamus_Proper... source mean =88.818, std = 23.3854 X:126-157; Y:125-155; Z:107-152 gca peak = 0.06537 (100) mri peak = 0.07538 (100) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (8424 voxels, overlap=0.589) aligning Right_Thalamus_Proper... source mean =87.8485, std = 25.0271 X:104-133; Y:125-156; Z:109-152 gca peak = 0.07019 (99) mri peak = 0.08722 (100) Right_Thalamus_Proper (49): linear fit = 1.05 x + 0.0 (6276 voxels, overlap=0.579) aligning Left_Putamen... source mean =93.842, std = 12.9543 X:137-168; Y:128-169; Z:120-167 gca peak = 0.09468 (90) mri peak = 0.09125 (102) Left_Putamen (12): linear fit = 1.12 x + 0.0 (4520 voxels, overlap=0.332) aligning Right_Putamen... source mean =96.7228, std = 13.8148 X:91-122; Y:130-169; Z:122-169 gca peak = 0.07184 (82) mri peak = 0.07456 (98) Right_Putamen (51): linear fit = 1.12 x + 0.0 (4843 voxels, overlap=0.393) aligning Left_Pallidum... source mean =104.76, std = 8.99533 X:137-160; Y:139-163; Z:126-157 gca peak = 0.11705 (100) mri peak = 0.17803 (107) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (1054 voxels, overlap=0.769) aligning Right_Pallidum... source mean =107.169, std = 9.37223 X:99-124; Y:139-163; Z:128-159 gca peak = 0.13501 (106) mri peak = 0.16765 (107) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (949 voxels, overlap=0.775) aligning Brain_Stem... source mean =72.5503, std = 26.6989 X:108-149; Y:144-226; Z:99-138 gca peak = 0.05597 (80) mri peak = 0.07249 (100) Brain_Stem (16): linear fit = 1.05 x + 0.0 (20178 voxels, overlap=0.394) aligning Right_VentralDC... source mean =87.4543, std = 26.2331 X:98-133; Y:144-175; Z:113-152 gca peak = 0.05879 (97) mri peak = 0.09475 (106) Right_VentralDC (60): linear fit = 1.02 x + 0.0 (2657 voxels, overlap=0.436) aligning Left_VentralDC... source mean =87.0562, std = 24.8565 X:126-161; Y:144-175; Z:113-152 gca peak = 0.06932 (98) mri peak = 0.09926 (106) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (3807 voxels, overlap=0.524) aligning Third_Ventricle... source mean =65.4984, std = 25.1088 X:124-135; Y:133-170; Z:117-154 gca peak = 0.10105 (38) mri peak = 0.08029 (106) overlap = 0, overlap_threshold = 0.001 insufficient overlap 0.0000 in histograms - rejecting aligning Fourth_Ventricle... source mean =63.3802, std = 26.0784 X:120-143; Y:150-215; Z:91-124 gca peak = 0.10426 (32) mri peak = 0.04958 (28) Fourth_Ventricle (15): linear fit = 1.62 x + 0.0 (1429 voxels, overlap=0.242) estimating mean gm scale to be 1.19 x + 0.0 estimating mean wm scale to be 0.99 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 writing gca to talairach.gca... Reinitialize GCAM with LTA rms after linear xform = 0.875 (5.301%) rms after linear xform = 0.800 (0.370%) rms after linear xform = 0.797 (-0.112%) rms increased - undoing step... rms after linear xform = 0.797 (0.000%) rms after linear xform = 0.797 (-0.112%) rms increased - undoing step... rms after linear xform = 0.797 (0.000%) rms after linear xform = 0.797 (-0.112%) rms increased - undoing step... rms after linear xform = 0.797 (0.000%) rms after linear xform = 0.797 (-0.122%) rms increased - undoing step... rms after linear xform = 0.797 (0.000%) 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... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 rms increased - undoing step... pct change < tol 0.025, nsmall = 2 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 pct change decreased switching integration type to fixed (done=1) pct change decreased rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 pct change decreased rms increased - undoing step... blurring input image with Gaussian with sigma=0.500... pct change decreased pct change decreased switching integration type to fixed (done=0) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased pct change decreased switching integration type to fixed (done=0) pct change decreased pct change decreased pct change decreased pct change decreased pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change decreased pct change < tol 0.025, nsmall = 2 of 2 switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... rms increased - undoing step... blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... pct change decreased switching integration type to fixed (done=0) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... pct change decreased switching integration type to fixed (done=0) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... pct change decreased switching integration type to fixed (done=0) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 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... rms increased - undoing step... blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) pct change decreased pct change < tol 0.025, nsmall = 1 of 2 pct change decreased rms increased - undoing step... pct change < tol 0.025, nsmall = 2 of 2 setting smoothness coefficient to 0.03 blurring input image with Gaussian with sigma=2.000... switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 0.12 blurring input image with Gaussian with sigma=2.000... switching integration type to fixed (done=1) pct change < tol 0.025, nsmall = 1 of 2 rms increased - undoing step... pct change < tol 0.025, nsmall = 2 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 setting smoothness coefficient to 0.40 blurring input image with Gaussian with sigma=2.000... switching integration type to fixed (done=1) pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 setting smoothness coefficient to 1.00 blurring input image with Gaussian with sigma=2.000... switching integration type to fixed (done=1) rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) pct change < tol 0.025, nsmall = 1 of 2 rms increased - undoing step... pct change < tol 0.025, nsmall = 2 of 2 resetting metric properties... setting smoothness coefficient to 2.00 blurring input image with Gaussian with sigma=2.000... switching integration type to fixed (done=1) pct change < tol 0.025, nsmall = 1 of 2 pct change < tol 0.025, nsmall = 2 of 2 blurring input image with Gaussian with sigma=0.500... switching integration type to fixed (done=1) starting rms=0.001, neg=1, removing folds in lattice.... iter 1, dt=229.376000: new neg 0, old_neg 1, delta 1, rms=0.001 rms increased - undoing step... pct change < tol 0.025, nsmall = 1 of 2 writing output transformation to transforms/talairach.m3z... registration took 501 minutes and 48 seconds. #-------------------------------------- #@# CA Reg Inv Sat Jul 15 00:50:13 EDT 2006 /usr/local/freesurfer/subjects/E_062/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z gcam->type = vox reading labels out of gcam file... Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Sat Jul 15 00:58:47 EDT 2006 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2006-02-15.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... Killed Linux dhcp-129-105-146-221.speech.northwestern.edu 2.4.22-10mdk #1 Thu Sep 18 12:30:58 CEST 2003 i686 unknown unknown GNU/Linux recon-all exited with ERRORS at Sat Jul 15 01:11:14 EDT 2006