Log file for surfreg Sun Jun 23 22:45:27 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 fsf18anat --t fsaverage_sym --lh --xhemi Linux compute-0-100 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux xhemireg --s fsf18anat outdir is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi Logfile is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/xhemireg.lh.log /space/crash/1/users/greve/freesurferx86/bin/xhemireg --s fsf18anat $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ Sun Jun 23 22:45:27 EDT 2013 Linux compute-0-100 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects Sun Jun 23 22:45:27 EDT 2013 Sun Jun 23 22:45:27 EDT 2013 mri_vol2vol --mov mri/orig.mgz --targ mri/orig.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/orig.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372298836 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/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/T1.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372184464 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/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/brain.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372721768 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/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/brainmask.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372673961 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/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/norm.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372760779 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/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/aseg.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372821630 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aseg.mgz --left-right-swap-label mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/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/fsf18anat/xhemi/mri/aseg.mgz... mri_vol2vol --mov mri/aparc+aseg.mgz --targ mri/aparc+aseg.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/aparc+aseg.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372137611 Resampling Output registration matrix is identity mri_vol2vol done mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aparc+aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aparc+aseg.mgz --left-right-swap-label mri_convert /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/mri/aparc+aseg.mgz /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/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/fsf18anat/xhemi/mri/aparc+aseg.mgz... mri_vol2vol --mov mri/nu.mgz --targ mri/nu.mgz --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat --o /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/mri/nu.mgz regfile /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 1372639795 Resampling Output registration matrix is identity mri_vol2vol done Sun Jun 23 22:46:52 EDT 2013 recon-all -sb fsf18anat/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-0-100 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux #-------------------------------------------- #@# Talairach Sun Jun 23 22:46:56 EDT 2013 /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:46:52 EDT 2013 Ended at Sun Jun 23 22:49:52 EDT 2013 #@#%# recon-all-run-time-hours 0.050 recon-all -s fsf18anat/xhemi finished without error at Sun Jun 23 22:49:52 EDT 2013 done Sun Jun 23 22:49:52 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz orig --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz orig --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:00 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz white --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz white --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:08 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz pial --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz pial --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:16 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz smoothwm --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz smoothwm --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:24 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz sphere --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz sphere --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:32 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz inflated --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz inflated --hemi lh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/rh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/lh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/label/rh.aparc.annot cp label/lh.BA.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/label/rh.BA.annot cp label/lh.aparc.a2009s.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/label/rh.aparc.a2009s.annot done hemi lh Logfile is /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/xhemireg.rh.log /space/crash/1/users/greve/freesurferx86/bin/xhemireg --s fsf18anat $Id: xhemireg,v 1.23 2012/06/04 15:00:51 greve Exp $ Sun Jun 23 22:50:40 EDT 2013 Linux compute-0-100 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.subjects Sun Jun 23 22:50:40 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz orig --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz orig --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.orig --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:47 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz white --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz white --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.white --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:50:54 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz pial --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz pial --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.pial --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:51:01 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz smoothwm --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz smoothwm --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.smoothwm --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:51:09 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz sphere --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz sphere --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.sphere --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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 22:51:16 EDT 2013 mri_surf2surf --s fsf18anat --sval-xyz inflated --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat mri_surf2surf --s fsf18anat --sval-xyz inflated --hemi rh --tval-xyz --tval /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.inflated --reg /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/lrrev.pure.register.dat sysname Linux hostname compute-0-100 machine x86_64 user greve srcsubject = fsf18anat srcval = (null) srctype = trgsubject = fsf18anat trgval = /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/surf/rh.sphere.reg Loading source data Reading surface file /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/label/lh.aparc.annot cp label/rh.BA.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/label/lh.BA.annot cp label/rh.aparc.a2009s.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/label/lh.aparc.a2009s.annot done hemi rh Sun Jun 23 22:51:24 EDT 2013 xhemireg done #@# lh Sun Jun 23 22:51:24 EDT 2013 #CMD# mris_register -curv -annot aparc.annot /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.sphere /space/freesurfer/subjects/fsfast-tutorial.subjects/fsaverage_sym/lh.reg.template.tif /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/xhemi/surf/lh.sphere /space/freesurfer/subjects/fsfast-tutorial.subjects/fsaverage_sym/lh.reg.template.tif /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/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/fsf18anat/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 = -0.001, std = 0.585 curvature mean = 0.053, std = 0.820 curvature mean = 0.020, std = 0.867 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, 0.00, 16.00) sse = 188893.3, tmin=1.3946 d=16.00 min @ (4.00, 0.00, 0.00) sse = 171047.0, tmin=4.2599 d=8.00 min @ (0.00, -2.00, -2.00) sse = 167162.2, tmin=5.6742 d=4.00 min @ (-1.00, 0.00, 0.00) sse = 166374.8, tmin=7.1140 d=2.00 min @ (0.50, 0.50, 0.00) sse = 166239.3, tmin=8.6220 d=1.00 min @ (-0.25, -0.25, 0.25) sse = 166126.9, tmin=10.0503 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 11.49 min curvature mean = 0.033, std = 0.852 curvature mean = 0.010, std = 0.943 curvature mean = 0.033, std = 0.866 curvature mean = 0.005, std = 0.975 curvature mean = 0.031, std = 0.869 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.026, std = 0.288 curvature mean = 0.038, std = 0.122 curvature mean = 0.069, std = 0.360 curvature mean = 0.036, std = 0.152 curvature mean = 0.037, std = 0.561 curvature mean = 0.037, std = 0.165 curvature mean = 0.021, std = 0.702 curvature mean = 0.037, std = 0.171 curvature mean = 0.007, std = 0.810 MRISregister() return, current seed 0 writing registered surface to /space/freesurfer/subjects/fsfast-tutorial.subjects/fsf18anat/xhemi/surf/lh.fsaverage_sym.sphere.reg... expanding nbhd size to 1 registration took 1.73 hours surfreg-Run-Time-Hours fsf18anat lh 1 1.83 Mon Jun 24 00:35:14 EDT 2013 surfreg done