Log file for surfreg Sun Jun 23 22:40:32 EDT 2013 setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/homes/004/greve/projects/nru /space/crash/1/users/greve/freesurferx86/bin/surfreg --s fsf11anat --t fsaverage_sym --lh --xhemi Linux compute-0-69 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux xhemireg --s fsf11anat outdir is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi Logfile is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/xhemireg.lh.log /space/crash/1/users/greve/freesurferx86/bin/xhemireg --s fsf11anat $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ Sun Jun 23 22:40:32 EDT 2013 Linux compute-0-69 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects Sun Jun 23 22:40:32 EDT 2013 Sun Jun 23 22:40:32 EDT 2013 mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/orig.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/orig.mgz targvol mri/orig.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/orig.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372369971 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/T1.mgz --targ mri/T1.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/T1.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/T1.mgz targvol mri/T1.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/T1.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372287877 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brain.mgz --targ mri/brain.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/brain.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/brain.mgz targvol mri/brain.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/brain.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372565585 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/brainmask.mgz --targ mri/brainmask.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/brainmask.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/brainmask.mgz targvol mri/brainmask.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/brainmask.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372560934 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/norm.mgz --targ mri/norm.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/norm.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/norm.mgz targvol mri/norm.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/norm.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372601883 Resampling Output registration matrix is identity mri_vol2vol done mri_vol2vol --mov mri/aseg.mgz --targ mri/aseg.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/aseg.mgz targvol mri/aseg.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372190433 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz --left-right-swap-label mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz --left-right-swap-label $Id: mri_convert.c,v 1.204 2013/06/05 17:00:52 fischl Exp $ reading from /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz... Performing left-right swap of labels TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.60053e-09, 3.87945e-08) j_ras = (1.95259e-16, -2.98023e-08, -1) k_ras = (1.49012e-08, 1, 2.98023e-08) writing to /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aseg.mgz... mri_vol2vol --mov mri/aparc+aseg.mgz --targ mri/aparc+aseg.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/aparc+aseg.mgz targvol mri/aparc+aseg.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision int (1) Gdiag_no -1 Synth 0 SynthSeed 1372366014 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz --left-right-swap-label mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz --left-right-swap-label $Id: mri_convert.c,v 1.204 2013/06/05 17:00:52 fischl Exp $ reading from /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz... Performing left-right swap of labels TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.60053e-09, 3.87945e-08) j_ras = (1.95259e-16, -2.98023e-08, -1) k_ras = (1.49012e-08, 1, 2.98023e-08) writing to /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/aparc+aseg.mgz... mri_vol2vol --mov mri/nu.mgz --targ mri/nu.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/nu.mgz --keep-precision --no-save-reg Matrix from regfile: -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; movvol mri/nu.mgz targvol mri/nu.mgz outvol /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri/nu.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision uchar (0) Gdiag_no -1 Synth 0 SynthSeed 1372141076 Resampling Output registration matrix is identity mri_vol2vol done Sun Jun 23 22:41:49 EDT 2013 recon-all -sb fsf11anat/xhemi -talairach Subject Stamp: freesurfer-x86_64-unknown-linux-gnu-dev5-20130607 Current Stamp: freesurfer-x86_64-unknown-linux-gnu-dev5-20130607 INFO: SUBJECTS_DIR is /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects Actual FREESURFER_HOME /autofs/space/crash_001/users/greve/freesurferx86 Linux compute-0-69 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Talairach Sun Jun 23 22:41:53 EDT 2013 /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #------------------------------------------ Started at Sun Jun 23 22:41:49 EDT 2013 Ended at Sun Jun 23 22:45:13 EDT 2013 #@#%# recon-all-run-time-hours 0.057 recon-all -s fsf11anat/xhemi finished without error at Sun Jun 23 22:45:13 EDT 2013 done Sun Jun 23 22:45:13 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz orig --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz orig --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.orig trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.orig Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:45:23 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz white --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz white --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.white trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.white Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:45:34 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz pial --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz pial --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.pial trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.pial Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:45:44 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz smoothwm --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz smoothwm --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.smoothwm trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.smoothwm Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:45:55 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz sphere --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz sphere --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.sphere trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere Applying linear registration transform -1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:46:06 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz inflated --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz inflated --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/rh.inflated trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/lh.inflated Applying linear registration transform -1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order cp label/lh.aparc.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/rh.aparc.annot cp label/lh.BA.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/rh.BA.annot cp label/lh.aparc.a2009s.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/rh.aparc.a2009s.annot done hemi lh Logfile is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/xhemireg.rh.log /space/crash/1/users/greve/freesurferx86/bin/xhemireg --s fsf11anat $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ Sun Jun 23 22:46:18 EDT 2013 Linux compute-0-69 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects Sun Jun 23 22:46:18 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz orig --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz orig --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.orig trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.orig Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:46:29 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz white --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz white --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.white trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.white Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:46:39 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz pial --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz pial --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.pial trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.pial Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:46:50 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz smoothwm --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz smoothwm --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.smoothwm trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.smoothwm Applying linear registration transform -1.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:47:00 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz sphere --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz sphere --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere Applying linear registration transform -1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order Sun Jun 23 22:47:10 EDT 2013 mri_surf2surf --s fsf11anat --sval-xyz inflated --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat $Id: mri_surf2surf.c,v 1.96 2012/08/28 13:59:38 greve Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects cd /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat mri_surf2surf --s fsf11anat --sval-xyz inflated --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-69 machine x86_64 user greve srcsubject = fsf11anat srcval = (null) srctype = trgsubject = fsf11anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.inflated trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = rh trghemi = rh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/surf/rh.inflated Applying linear registration transform -1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Determinant of linear transform is negative, so reversing face order INFO: trgsubject = srcsubject Saving target data Reversing Face Order cp label/rh.aparc.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/lh.aparc.annot cp label/rh.BA.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/lh.BA.annot cp label/rh.aparc.a2009s.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/label/lh.aparc.a2009s.annot done hemi rh Sun Jun 23 22:47:22 EDT 2013 xhemireg done #@# lh Sun Jun 23 22:47:22 EDT 2013 #CMD# mris_register -curv -annot aparc.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere /space/freesurfer/subjects/fsfast-tutorial.subjects/fsaverage_sym/lh.reg.template.tif /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot cwd /autofs/homes/004/greve/projects/nru cmdline mris_register -curv -annot aparc.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere /space/freesurfer/subjects/fsfast-tutorial.subjects/fsaverage_sym/lh.reg.template.tif /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.fsaverage_sym.sphere.reg 0 inflated.H 1 sulc 2 (null) $Id: mris_register.c,v 1.61 2013/01/15 17:19:03 greve Exp $ $Id: mrisurf.c,v 1.751 2013/05/17 18:25:08 fischl Exp $ reading surface from /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.sphere... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading template parameterization from /space/freesurfer/subjects/fsfast-tutorial.subjects/fsaverage_sym/lh.reg.template.tif... ripping medial wall... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = 0.003, std = 0.563 curvature mean = 0.038, std = 0.806 curvature mean = 0.026, std = 0.836 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 0.00) sse = 256860.5, tmin=2.0018 d=32.00 min @ (-8.00, -8.00, 0.00) sse = 251983.2, tmin=4.0641 d=16.00 min @ (4.00, 4.00, 0.00) sse = 229906.8, tmin=6.1744 d=8.00 min @ (-2.00, -2.00, 2.00) sse = 226297.6, tmin=8.3051 d=4.00 min @ (1.00, 1.00, 0.00) sse = 223848.3, tmin=10.4594 d=2.00 min @ (0.00, 0.00, -0.50) sse = 223690.4, tmin=12.7174 d=1.00 min @ (0.00, 0.00, 0.25) sse = 223648.8, tmin=14.9753 d=0.50 min @ (0.00, 0.00, -0.12) sse = 223626.6, tmin=17.2343 tol=1.0e+00, sigma=0.5, host=compu, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 17.23 min curvature mean = 0.008, std = 0.816 curvature mean = 0.011, std = 0.925 curvature mean = 0.005, std = 0.828 curvature mean = 0.005, std = 0.966 curvature mean = 0.004, std = 0.830 curvature mean = 0.002, std = 0.985 2 Reading smoothwm curvature mean = -0.024, std = 0.283 curvature mean = 0.036, std = 0.120 curvature mean = 0.065, std = 0.346 curvature mean = 0.034, std = 0.149 curvature mean = 0.033, std = 0.554 curvature mean = 0.034, std = 0.163 curvature mean = 0.017, std = 0.708 curvature mean = 0.034, std = 0.169 curvature mean = 0.006, std = 0.821 MRISregister() return, current seed 0 writing registered surface to /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf11anat/xhemi/surf/lh.fsaverage_sym.sphere.reg... expanding nbhd size to 1 registration took 2.72 hours surfreg-Run-Time-Hours fsf11anat lh 1 2.84 Mon Jun 24 01:30:52 EDT 2013 surfreg done