Log file is /home/tylers/bbreg_test/init-fsl/fsl_register.dat.log Thu Mar 17 14:50:28 PDT 2011 setenv SUBJECTS_DIR /home/tylers/bbreg_test cd /home/tylers/bbreg_test/init-fsl.old /home/tylers/apps/freesurfer//bin/bbregister --s hd2155v1 --mov /home/tylers/bbreg_test/T2brain.nii.gz --reg /home/tylers/bbreg_test/init-fsl/fsl_register.dat --init-fsl --t2 $Id: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Exp $ Linux perirhinal.ucsd.edu 2.6.9-89.31.1.ELsmp #1 SMP Mon Oct 4 21:41:59 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /home/tylers/apps/freesurfer/ mri_convert /home/tylers/bbreg_test/T2brain.nii.gz /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii mri_convert /home/tylers/bbreg_test/T2brain.nii.gz /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/tylers/bbreg_test/T2brain.nii.gz... TR=1000.00, 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 /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii... fslregister --s hd2155v1 --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister --dof 6 Log file is /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat.fslregister.log Thu Mar 17 14:50:28 PDT 2011 --s hd2155v1 --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister --dof 6 $Id: fslregister,v 1.16.2.2 2009/07/31 22:24:05 greve Exp $ perirhinal.ucsd.edu Linux perirhinal.ucsd.edu 2.6.9-89.31.1.ELsmp #1 SMP Mon Oct 4 21:41:59 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/tylers/bbreg_test/init-fsl.old mri_convert /home/tylers/bbreg_test/hd2155v1/mri/brainmask.mgz /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/refvol.fslregister.nii mri_convert /home/tylers/bbreg_test/hd2155v1/mri/brainmask.mgz /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/tylers/bbreg_test/hd2155v1/mri/brainmask.mgz... TR=6.50, TE=2.80, TI=600.00, flip angle=687.55 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/refvol.fslregister.nii... -------------------------------------- /home/tylers/bbreg_test/init-fsl.old mri_convert /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii... TR=1000.00, 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) keeping frame 0 writing to /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii... /home/tylers/bbreg_test/init-fsl.old tkregister2_cmdl --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii --reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/reg0.16260.dat --regheader --fslregout /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat.fsl.mat0 --s hd2155v1 --noedit tkregister_tcl /home/tylers/apps/freesurfer//lib/tcl/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii reg file /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/reg0.16260.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /home/tylers/bbreg_test/hd2155v1/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.859 0.000 0.000 110.003; 0.000 0.000 4.000 -64.000; 0.000 -0.859 0.000 110.003; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 0.000 0.000 -0.909; 0.000 0.000 1.000 -20.317; 0.000 -1.000 0.000 37.134; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -0.909; 0.000 0.000 1.000 -20.317; 0.000 -1.000 0.000 37.134; 0.000 0.000 0.000 1.000; Determinant 1 subject = hd2155v1 RegMat --------------------------- 1.000 0.000 0.000 -0.909; 0.000 0.000 1.000 -20.317; 0.000 -1.000 0.000 37.134; 0.000 0.000 0.000 1.000; register: file /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/reg0.16260.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -2.95427, ref det = -1 Thu Mar 17 14:50:32 PDT 2011 /home/tylers/bbreg_test/init-fsl.old flirt -ref /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/refvol.fslregister.nii -in /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/fslregister/movvol.fslregister.nii -bins 256 -omat /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat.fsl.mat -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -schedule /home/tylers/apps/freesurfer//bin/flirt.newdefault.20080811.sch -init /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat.fsl.mat0 tkregister2_cmdl --s hd2155v1 --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --fslreg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat.fsl.mat --noedit tkregister_tcl /home/tylers/apps/freesurfer//lib/tcl/tkregister2.tcl ---- FSL registration matrix -------- 0.939 0.000 0.345 11.611; 0.313 -0.424 -0.850 163.894; 0.146 0.905 -0.398 15.875; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii reg file /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /home/tylers/bbreg_test/hd2155v1/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii Tmov: -------------------- -0.859 0.000 0.000 110.003; 0.000 0.000 4.000 -64.000; 0.000 -0.859 0.000 110.003; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -2.95427, ref det = -1 ---- Input registration matrix (computed) -------- 0.939 -0.146 0.313 -4.393; -0.345 -0.398 0.850 -38.019; 0.000 -0.905 -0.424 -6.810; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.939 -0.146 0.313 -4.393; -0.345 -0.398 0.850 -38.019; 0.000 -0.905 -0.424 -6.810; 0.000 0.000 0.000 1.000; Determinant 1 subject = hd2155v1 RegMat --------------------------- 0.939 -0.146 0.313 -4.393; -0.345 -0.398 0.850 -38.019; 0.000 -0.905 -0.424 -6.810; 0.000 0.000 0.000 1.000; register: file /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat written Started at Thu Mar 17 14:50:28 PDT 2011 Ended at Thu Mar 17 14:52:01 PDT 2011 fslregister Done To check results, run: tkregister2 --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --surf orig mri_segreg --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --init-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --out-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.70.2.7 2009/07/29 22:52:38 nicks Exp $ setenv SUBJECTS_DIR /home/tylers/bbreg_test cd /home/tylers/bbreg_test/init-fsl.old mri_segreg --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --init-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat --out-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname perirhinal.ucsd.edu machine x86_64 user tylers movvol /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii regfile /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.init.dat subject hd2155v1 dof 6 outregfile /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 100 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 DoPowell 1 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1300863800 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.939 -0.146 0.313 -4.393; -0.345 -0.398 0.850 -38.019; 0.000 -0.905 -0.424 -6.810; 0.000 0.000 0.000 1.000; Loading mov Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting LH Surfs Projecting RH Surfs Loading rh.white surf Loading rh.thickness No such file or directory mri_segreg: could not open label file /home/tylers/bbreg_test/hd2155v1/label/lh.cortex.label Projecting RH Surfs lh.cortex.label /home/tylers/bbreg_test/hd2155v1/label/lh.cortex.label Invalid argument No such file or directory mri_segreg: could not open label file /home/tylers/bbreg_test/hd2155v1/label/rh.cortex.label Warning cannot find lh.cortex.label ... continuing rh.cortex.label /home/tylers/bbreg_test/hd2155v1/label/rh.cortex.label No such file or directory Warning cannot find rh.cortex.label ... continuing Computing relative cost 0 -25.0 -25.0 -25.0 1.028020 1 -25.0 -25.0 25.0 1.025491 2 -25.0 25.0 -25.0 1.068716 3 -25.0 25.0 25.0 0.958504 4 25.0 -25.0 -25.0 1.028126 5 25.0 -25.0 25.0 0.940412 6 25.0 25.0 -25.0 0.995338 7 25.0 25.0 25.0 1.000761 REL: 8 0.964696 8.045366 1.005671 rel = 0.959256 Initial costs ---------------- Number of surface hits 0 WM Intensity 0.0000 +/- 0.0000 Ctx Intensity 0.0000 +/- 0.0000 Pct Contrast 0.0000 +/- 0.0000 Cost 0.0000 RelCost 0.9593 ------------------------------------ Bruce force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0011 1.0011 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9980 0.9980 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9629 0.9629 0.0 11 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.9612 0.9612 0.0 12 -4.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9592 0.9592 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.9445 0.9445 0.0 27 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.9355 0.9355 0.0 104 -4.0000 0.0000 -4.0000 4.0000 0.0000 4.0000 0.9219 0.9219 0.0 249 0.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9150 0.9150 0.0 258 0.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.9146 0.9146 0.0 272 0.0000 -4.0000 0.0000 -4.0000 -4.0000 4.0000 0.8936 0.8936 0.0 513 4.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.8813 0.8813 0.1 516 4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8509 0.8509 0.1 Brute Force -------------------------- Min cost was 0.850915 Number of iterations 729 Search time 5.720000 sec Parameters at best (transmm, rotdeg) 4.000 -4.000 0.000 -4.000 0.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 4 1 -4 2 0 3 -4 4 0 5 -4 7 4.018 -4.000 0.000 -4.000 0.000 -4.000 0.8494828385 8 4.156 -4.000 0.000 -4.000 0.000 -4.000 0.8462716224 10 4.124 -4.000 0.000 -4.000 0.000 -4.000 0.8459969581 11 4.126 -4.000 0.000 -4.000 0.000 -4.000 0.8459862838 12 4.131 -4.000 0.000 -4.000 0.000 -4.000 0.8459738668 14 4.130 -4.000 0.000 -4.000 0.000 -4.000 0.8459735304 15 4.130 -4.000 0.000 -4.000 0.000 -4.000 0.8459731588 16 4.130 -4.000 0.000 -4.000 0.000 -4.000 0.8459730863 24 4.130 -3.925 0.000 -4.000 0.000 -4.000 0.8445271625 26 4.130 -3.914 0.000 -4.000 0.000 -4.000 0.8445167771 27 4.130 -3.916 0.000 -4.000 0.000 -4.000 0.8445145653 28 4.130 -3.917 0.000 -4.000 0.000 -4.000 0.8445144029 29 4.130 -3.917 0.000 -4.000 0.000 -4.000 0.8445143540 31 4.130 -3.917 0.000 -4.000 0.000 -4.000 0.8445143256 40 4.130 -3.917 -0.028 -4.000 0.000 -4.000 0.8442903481 41 4.130 -3.917 -0.035 -4.000 0.000 -4.000 0.8442793021 45 4.130 -3.917 -0.035 -4.000 0.000 -4.000 0.8442793006 53 4.130 -3.917 -0.035 -3.989 0.000 -4.000 0.8441649146 55 4.130 -3.917 -0.035 -3.969 0.000 -4.000 0.8440876743 58 4.130 -3.917 -0.035 -3.967 0.000 -4.000 0.8440872445 59 4.130 -3.917 -0.035 -3.968 0.000 -4.000 0.8440858878 73 4.130 -3.917 -0.035 -3.968 -0.001 -4.000 0.8440857244 76 4.130 -3.917 -0.035 -3.968 -0.000 -4.000 0.8440856718 80 4.130 -3.917 -0.035 -3.968 -0.000 -4.000 0.8440855980 81 4.130 -3.917 -0.035 -3.968 -0.000 -4.000 0.8440853974 88 4.130 -3.917 -0.035 -3.968 -0.000 -4.000 0.8440853748 98 4.130 -3.917 -0.035 -3.968 -0.000 -3.989 0.8440106164 99 4.130 -3.917 -0.035 -3.968 -0.000 -3.975 0.8439800252 100 4.130 -3.917 -0.035 -3.968 -0.000 -3.976 0.8439769917 101 4.130 -3.917 -0.035 -3.968 -0.000 -3.979 0.8439763041 103 4.130 -3.917 -0.035 -3.968 -0.000 -3.978 0.8439758206 104 4.130 -3.917 -0.035 -3.968 -0.000 -3.978 0.8439754905 108 4.130 -3.917 -0.035 -3.968 -0.000 -3.978 0.8439754195 120 4.098 -3.917 -0.035 -3.968 -0.000 -3.978 0.8436922368 122 4.105 -3.917 -0.035 -3.968 -0.000 -3.978 0.8436691181 123 4.105 -3.917 -0.035 -3.968 -0.000 -3.978 0.8436690398 124 4.105 -3.917 -0.035 -3.968 -0.000 -3.978 0.8436689993 134 4.105 -3.894 -0.035 -3.968 -0.000 -3.978 0.8432482782 135 4.105 -3.833 -0.035 -3.968 -0.000 -3.978 0.8428572051 136 4.105 -3.840 -0.035 -3.968 -0.000 -3.978 0.8428391036 137 4.105 -3.844 -0.035 -3.968 -0.000 -3.978 0.8428344875 139 4.105 -3.848 -0.035 -3.968 -0.000 -3.978 0.8428336920 140 4.105 -3.847 -0.035 -3.968 -0.000 -3.978 0.8428330158 141 4.105 -3.847 -0.035 -3.968 -0.000 -3.978 0.8428330128 142 4.105 -3.847 -0.035 -3.968 -0.000 -3.978 0.8428329107 158 4.105 -3.846 -0.042 -3.968 -0.000 -3.978 0.8427669344 160 4.105 -3.846 -0.046 -3.968 -0.000 -3.978 0.8427555145 161 4.105 -3.846 -0.047 -3.968 -0.000 -3.978 0.8427554670 162 4.105 -3.846 -0.046 -3.968 -0.000 -3.978 0.8427554558 177 4.105 -3.846 -0.046 -3.933 -0.000 -3.978 0.8422840556 178 4.105 -3.846 -0.046 -3.930 -0.000 -3.978 0.8422805834 193 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422783675 194 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422783497 195 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422781977 196 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422781338 198 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422781253 199 4.105 -3.846 -0.046 -3.930 0.002 -3.978 0.8422779614 210 4.105 -3.846 -0.046 -3.930 0.002 -3.936 0.8419193137 211 4.105 -3.846 -0.046 -3.930 0.002 -3.934 0.8419178635 212 4.105 -3.846 -0.046 -3.930 0.002 -3.933 0.8419176277 218 4.079 -3.775 -0.057 -3.893 0.005 -3.888 0.8417458631 245 4.093 -3.774 -0.046 -3.930 0.002 -3.933 0.8416379561 247 4.093 -3.805 -0.046 -3.930 0.002 -3.933 0.8411661830 249 4.093 -3.800 -0.046 -3.930 0.002 -3.933 0.8411298464 250 4.093 -3.790 -0.046 -3.930 0.002 -3.933 0.8411223571 251 4.093 -3.794 -0.046 -3.930 0.002 -3.933 0.8411114819 253 4.093 -3.794 -0.046 -3.930 0.002 -3.933 0.8411113657 257 4.093 -3.794 -0.046 -3.930 0.002 -3.933 0.8411113555 266 4.093 -3.794 -0.043 -3.930 0.002 -3.933 0.8410853886 268 4.093 -3.794 -0.042 -3.930 0.002 -3.933 0.8410848282 269 4.093 -3.794 -0.042 -3.930 0.002 -3.933 0.8410846734 287 4.093 -3.794 -0.042 -3.925 0.002 -3.933 0.8410370322 289 4.093 -3.794 -0.042 -3.927 0.002 -3.933 0.8410330924 290 4.093 -3.794 -0.042 -3.926 0.002 -3.933 0.8410305914 291 4.093 -3.794 -0.042 -3.926 0.002 -3.933 0.8410303957 298 4.093 -3.794 -0.042 -3.926 0.002 -3.933 0.8410303457 306 4.093 -3.794 -0.042 -3.926 -0.007 -3.933 0.8410184643 308 4.093 -3.794 -0.042 -3.926 -0.003 -3.933 0.8410091980 315 4.093 -3.794 -0.042 -3.926 -0.003 -3.933 0.8410088864 328 4.093 -3.794 -0.042 -3.926 -0.003 -3.904 0.8409613859 329 4.093 -3.794 -0.042 -3.926 -0.003 -3.913 0.8409352065 330 4.093 -3.794 -0.042 -3.926 -0.003 -3.915 0.8409344415 349 4.092 -3.794 -0.042 -3.926 -0.003 -3.915 0.8409330419 350 4.088 -3.794 -0.042 -3.926 -0.003 -3.915 0.8409288919 352 4.090 -3.794 -0.042 -3.926 -0.003 -3.915 0.8409280019 369 4.090 -3.791 -0.042 -3.926 -0.003 -3.915 0.8409042986 370 4.090 -3.776 -0.042 -3.926 -0.003 -3.915 0.8408460889 371 4.090 -3.776 -0.042 -3.926 -0.003 -3.915 0.8408458706 372 4.090 -3.778 -0.042 -3.926 -0.003 -3.915 0.8408455650 374 4.090 -3.777 -0.042 -3.926 -0.003 -3.915 0.8408454138 390 4.090 -3.777 -0.041 -3.926 -0.003 -3.915 0.8408449340 391 4.090 -3.777 -0.041 -3.926 -0.003 -3.915 0.8408448490 394 4.090 -3.777 -0.041 -3.926 -0.003 -3.915 0.8408447125 410 4.090 -3.777 -0.041 -3.924 -0.003 -3.915 0.8407998750 411 4.090 -3.777 -0.041 -3.921 -0.003 -3.915 0.8407971878 412 4.090 -3.777 -0.041 -3.922 -0.003 -3.915 0.8407875972 413 4.090 -3.777 -0.041 -3.922 -0.003 -3.915 0.8407874886 427 4.090 -3.777 -0.041 -3.922 -0.007 -3.915 0.8407731230 428 4.090 -3.777 -0.041 -3.922 -0.008 -3.915 0.8407719327 431 4.090 -3.777 -0.041 -3.922 -0.007 -3.915 0.8407717998 440 4.090 -3.777 -0.041 -3.922 -0.007 -3.915 0.8407717548 450 4.090 -3.777 -0.041 -3.922 -0.007 -3.907 0.8407495925 462 4.086 -3.760 -0.041 -3.918 -0.012 -3.900 0.8407413887 492 4.090 -3.774 -0.041 -3.922 -0.007 -3.907 0.8407401391 493 4.090 -3.773 -0.041 -3.922 -0.007 -3.907 0.8407394060 494 4.090 -3.772 -0.041 -3.922 -0.007 -3.907 0.8407386024 513 4.090 -3.772 -0.041 -3.922 -0.007 -3.907 0.8407383873 514 4.090 -3.772 -0.041 -3.922 -0.007 -3.907 0.8407382832 533 4.090 -3.772 -0.041 -3.922 -0.007 -3.907 0.8407382462 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.007113 1 -25.0 -25.0 25.0 0.985431 2 -25.0 25.0 -25.0 0.991867 3 -25.0 25.0 25.0 1.001321 4 25.0 -25.0 -25.0 0.996960 5 25.0 -25.0 25.0 1.017391 6 25.0 25.0 -25.0 0.998601 7 25.0 25.0 25.0 1.019902 REL: 8 0.840738 8.018586 1.002323 rel = 0.83879 Number of iterations 4 Min cost was 0.840738 Number of FunctionCalls 618 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 4.953000 sec Parameters at optimum (transmm, rotdeg) 4.09014 -3.77162 -0.04095 -3.92208 -0.00739 -3.90708 Costs at optimum 2144 823.4925 264.6301 29.0210 854.8015 300.2433 2.4844 0.8407 Reg at min cost was 0.913 -0.177 0.368 -2.908; -0.407 -0.448 0.796 -41.779; 0.024 -0.876 -0.482 -4.235; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat Original Reg 0.939 -0.146 0.313 -4.393; -0.345 -0.398 0.850 -38.019; 0.000 -0.905 -0.424 -6.810; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.026 0.031 -0.055 -1.485; 0.062 0.050 0.054 3.760; -0.024 -0.029 0.057 -2.575; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 5.382878 Computing change in rh position Surface RMS Diff (mm) 5.761941 9.763022 mri_segreg done mri_segreg --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --init-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat --out-reg /home/tylers/bbreg_test/init-fsl/fsl_register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/tylers/bbreg_test/init-fsl/fsl_register.dat.mincost --dof 6 --cur-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.70.2.7 2009/07/29 22:52:38 nicks Exp $ setenv SUBJECTS_DIR /home/tylers/bbreg_test cd /home/tylers/bbreg_test/init-fsl.old mri_segreg --mov /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii --init-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat --out-reg /home/tylers/bbreg_test/init-fsl/fsl_register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/tylers/bbreg_test/init-fsl/fsl_register.dat.mincost --dof 6 --cur-reg /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname perirhinal.ucsd.edu machine x86_64 user tylers movvol /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/template.nii regfile /home/tylers/bbreg_test/init-fsl/tmp.bbregister.16224/bbr.pass1.dat subject hd2155v1 dof 6 outregfile /home/tylers/bbreg_test/init-fsl/fsl_register.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 DoPowell 1 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1301249033 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.913 -0.177 0.368 -2.908; -0.407 -0.448 0.796 -41.779; 0.024 -0.876 -0.482 -4.235; 0.000 0.000 0.000 1.000; Loading mov Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting LH Surfs Projecting RH Surfs Loading rh.white surf Loading rh.thickness No such file or directory mri_segreg: could not open label file /home/tylers/bbreg_test/hd2155v1/label/lh.cortex.label Projecting RH Surfs lh.cortex.label /home/tylers/bbreg_test/hd2155v1/label/lh.cortex.label Invalid argument No such file or directory mri_segreg: could not open label file /home/tylers/bbreg_test/hd2155v1/label/rh.cortex.label Warning cannot find lh.cortex.label ... continuing rh.cortex.label /home/tylers/bbreg_test/hd2155v1/label/rh.cortex.label No such file or directory Warning cannot find rh.cortex.label ... continuing Computing relative cost 0 -25.0 -25.0 -25.0 0.975698 1 -25.0 -25.0 25.0 1.003999 2 -25.0 25.0 -25.0 1.015246 3 -25.0 25.0 25.0 0.999310 4 25.0 -25.0 -25.0 0.996529 5 25.0 -25.0 25.0 1.018626 6 25.0 25.0 -25.0 1.007601 7 25.0 25.0 25.0 1.021453 REL: 8 0.904758 8.038461 1.004808 rel = 0.900429 Initial costs ---------------- Number of surface hits 0 WM Intensity 0.0000 +/- 0.0000 Ctx Intensity 0.0000 +/- 0.0000 Pct Contrast 0.0000 +/- 0.0000 Cost 0.0000 RelCost 0.9004 ------------------------------------ Bruce force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8558 0.8558 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8542 0.8542 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8533 0.8533 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.8522 0.8522 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.8504 0.8504 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8488 0.8488 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8486 0.8486 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.8470 0.8470 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.8458 0.8458 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.8454 0.8454 0.0 42 -0.1000 -0.1000 0.0000 0.0000 0.1000 -0.1000 0.8442 0.8442 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.8434 0.8434 0.0 123 -0.1000 0.0000 0.0000 0.0000 0.1000 -0.1000 0.8427 0.8427 0.0 132 -0.1000 0.0000 0.0000 0.1000 0.1000 -0.1000 0.8424 0.8424 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8407 0.8407 0.0 Brute Force -------------------------- Min cost was 0.840739 Number of iterations 729 Search time 5.628000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 9 -0.055 0.000 0.000 0.000 0.000 0.000 0.9046830915 10 -0.062 0.000 0.000 0.000 0.000 0.000 0.9046721816 12 -0.084 0.000 0.000 0.000 0.000 0.000 0.9046653804 13 -0.076 0.000 0.000 0.000 0.000 0.000 0.9046616687 17 -0.077 0.000 0.000 0.000 0.000 0.000 0.9046601696 23 -0.077 1.000 0.000 0.000 0.000 0.000 0.8992215046 24 -0.077 2.618 0.000 0.000 0.000 0.000 0.8953754795 31 -0.077 2.613 0.000 0.000 0.000 0.000 0.8953684148 33 -0.077 2.601 0.000 0.000 0.000 0.000 0.8953624619 39 -0.077 2.601 -1.618 0.000 0.000 0.000 0.8849128822 43 -0.077 2.601 -1.382 0.000 0.000 0.000 0.8848986557 44 -0.077 2.601 -1.494 0.000 0.000 0.000 0.8848395274 46 -0.077 2.601 -1.446 0.000 0.000 0.000 0.8847927479 48 -0.077 2.601 -1.455 0.000 0.000 0.000 0.8847866119 50 -0.077 2.601 -1.453 0.000 0.000 0.000 0.8847814496 58 -0.077 2.601 -1.453 0.110 0.000 0.000 0.8847570198 61 -0.077 2.601 -1.453 0.149 0.000 0.000 0.8847514480 62 -0.077 2.601 -1.453 0.133 0.000 0.000 0.8847494262 64 -0.077 2.601 -1.453 0.124 0.000 0.000 0.8847433224 65 -0.077 2.601 -1.453 0.119 0.000 0.000 0.8847390074 67 -0.077 2.601 -1.453 0.119 0.000 0.000 0.8847383345 68 -0.077 2.601 -1.453 0.121 0.000 0.000 0.8847366295 73 -0.077 2.601 -1.453 0.121 0.000 0.000 0.8847365034 74 -0.077 2.601 -1.453 0.122 0.000 0.000 0.8847364103 81 -0.077 2.601 -1.453 0.122 0.144 0.000 0.8846185269 82 -0.077 2.601 -1.453 0.122 0.151 0.000 0.8846077450 83 -0.077 2.601 -1.453 0.122 0.239 0.000 0.8844470173 85 -0.077 2.601 -1.453 0.122 0.222 0.000 0.8844258881 89 -0.077 2.601 -1.453 0.122 0.220 0.000 0.8844233916 94 -0.077 2.601 -1.453 0.122 0.220 0.000 0.8844231815 96 -0.077 2.601 -1.453 0.122 0.220 1.000 0.8823285380 100 -0.077 2.601 -1.453 0.122 0.220 0.618 0.8817983972 103 -0.077 2.601 -1.453 0.122 0.220 0.636 0.8817972162 104 -0.077 2.601 -1.453 0.122 0.220 0.630 0.8817885068 105 -0.077 2.601 -1.453 0.122 0.220 0.627 0.8817859766 108 -0.077 2.601 -1.453 0.122 0.220 0.626 0.8817845512 118 -0.334 2.601 -1.453 0.122 0.220 0.626 0.8812410522 119 -0.328 2.601 -1.453 0.122 0.220 0.626 0.8812339670 120 -0.285 2.601 -1.453 0.122 0.220 0.626 0.8812263464 122 -0.269 2.601 -1.453 0.122 0.220 0.626 0.8812236780 123 -0.245 2.601 -1.453 0.122 0.220 0.626 0.8811817122 125 -0.245 2.601 -1.453 0.122 0.220 0.626 0.8811813598 128 -0.246 2.601 -1.453 0.122 0.220 0.626 0.8811798775 139 -0.246 2.626 -1.453 0.122 0.220 0.626 0.8811255843 141 -0.246 2.657 -1.453 0.122 0.220 0.626 0.8810820486 146 -0.246 2.658 -1.453 0.122 0.220 0.626 0.8810813853 149 -0.246 2.658 -1.453 0.122 0.220 0.626 0.8810812408 150 -0.246 2.659 -1.453 0.122 0.220 0.626 0.8810811437 151 -0.246 2.659 -1.453 0.122 0.220 0.626 0.8810811136 166 -0.246 2.659 -1.454 0.122 0.220 0.626 0.8810810499 167 -0.246 2.659 -1.455 0.122 0.220 0.626 0.8810751521 172 -0.246 2.659 -1.455 0.122 0.220 0.626 0.8810751507 188 -0.246 2.659 -1.455 0.123 0.220 0.626 0.8810730468 192 -0.246 2.659 -1.455 0.123 0.220 0.626 0.8810728075 193 -0.246 2.659 -1.455 0.124 0.220 0.626 0.8810726708 194 -0.246 2.659 -1.455 0.124 0.220 0.626 0.8810726230 195 -0.246 2.659 -1.455 0.124 0.220 0.626 0.8810725458 198 -0.246 2.659 -1.455 0.124 0.220 0.626 0.8810725438 199 -0.246 2.659 -1.455 0.124 0.220 0.626 0.8810725351 209 -0.246 2.659 -1.455 0.124 0.255 0.626 0.8810329172 210 -0.246 2.659 -1.455 0.124 0.256 0.626 0.8810320763 211 -0.246 2.659 -1.455 0.124 0.278 0.626 0.8810160151 213 -0.246 2.659 -1.455 0.124 0.274 0.626 0.8810131295 214 -0.246 2.659 -1.455 0.124 0.267 0.626 0.8810123468 217 -0.246 2.659 -1.455 0.124 0.266 0.626 0.8810077773 222 -0.246 2.659 -1.455 0.124 0.266 0.626 0.8810076340 224 -0.246 2.659 -1.455 0.124 0.266 0.626 0.8810075866 233 -0.246 2.659 -1.455 0.124 0.266 0.647 0.8809994854 235 -0.246 2.659 -1.455 0.124 0.266 0.648 0.8809994705 257 -0.247 2.659 -1.455 0.124 0.266 0.648 0.8809964253 260 -0.247 2.659 -1.455 0.124 0.266 0.648 0.8809957664 263 -0.247 2.659 -1.455 0.124 0.266 0.648 0.8809956327 279 -0.247 2.645 -1.455 0.124 0.266 0.648 0.8809814051 283 -0.247 2.646 -1.455 0.124 0.266 0.648 0.8809794958 284 -0.247 2.647 -1.455 0.124 0.266 0.648 0.8809792685 286 -0.247 2.647 -1.455 0.124 0.266 0.648 0.8809787193 287 -0.247 2.647 -1.455 0.124 0.266 0.648 0.8809783794 290 -0.247 2.647 -1.455 0.124 0.266 0.648 0.8809782970 291 -0.247 2.647 -1.455 0.124 0.266 0.648 0.8809782505 307 -0.247 2.647 -1.446 0.124 0.266 0.648 0.8809774772 308 -0.247 2.647 -1.449 0.124 0.266 0.648 0.8809772530 309 -0.247 2.647 -1.449 0.124 0.266 0.648 0.8809772432 333 -0.247 2.647 -1.449 0.124 0.266 0.648 0.8809768758 335 -0.247 2.647 -1.449 0.125 0.266 0.648 0.8809766000 338 -0.247 2.647 -1.449 0.125 0.266 0.648 0.8809765702 344 -0.247 2.647 -1.449 0.125 0.266 0.648 0.8809765629 372 -0.247 2.647 -1.449 0.125 0.266 0.648 0.8809765607 500 -0.247 2.647 -1.449 0.125 0.266 0.648 0.8809765566 539 -0.247 2.647 -1.448 0.125 0.266 0.648 0.8809765277 567 -0.247 2.647 -1.448 0.126 0.266 0.648 0.8809761851 572 -0.247 2.647 -1.448 0.126 0.266 0.648 0.8809761227 573 -0.247 2.647 -1.448 0.126 0.266 0.648 0.8809761174 576 -0.247 2.647 -1.448 0.126 0.266 0.648 0.8809761113 644 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809759002 653 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809758945 655 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809758900 720 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809758747 749 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809758268 849 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809757983 851 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809757834 929 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809756965 930 -0.247 2.647 -1.447 0.127 0.266 0.648 0.8809756954 951 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756277 956 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756176 1020 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756147 1045 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756120 1051 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756081 1052 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809756020 1166 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809755971 1256 -0.247 2.647 -1.448 0.127 0.266 0.648 0.8809755948 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.995717 1 -25.0 -25.0 25.0 1.014142 2 -25.0 25.0 -25.0 1.018722 3 -25.0 25.0 25.0 0.992833 4 25.0 -25.0 -25.0 1.004860 5 25.0 -25.0 25.0 1.011108 6 25.0 25.0 -25.0 0.996591 7 25.0 25.0 25.0 1.028401 REL: 8 0.880976 8.062374 1.007797 rel = 0.87416 Number of iterations 6 Min cost was 0.880976 Number of FunctionCalls 1281 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 273.445000 sec Parameters at optimum (transmm, rotdeg) -0.24738 2.64728 -1.44824 0.12708 0.26594 0.64792 Costs at optimum 216333 838.1174 276.2519 30.7750 864.9962 302.8265 2.1854 0.8810 Reg at min cost was 0.918 -0.176 0.356 -2.703; -0.397 -0.449 0.801 -39.152; 0.019 -0.876 -0.481 -5.763; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/tylers/bbreg_test/init-fsl/fsl_register.dat Original Reg 0.913 -0.177 0.368 -2.908; -0.407 -0.448 0.796 -41.779; 0.024 -0.876 -0.482 -4.235; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.005 -0.001 0.011 -0.205; -0.010 0.000 -0.005 -2.626; 0.005 0.000 -0.000 1.527; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 2.820660 Computing change in rh position Surface RMS Diff (mm) 3.119776 3.826480 mri_segreg done Cleaning up Started at Thu Mar 17 14:50:28 PDT 2011 Ended at Thu Mar 17 14:57:21 PDT 2011 BBR-Run-Time-Sec 413 bbregister Done To check results, run: tkregister2 --mov /home/tylers/bbreg_test/T2brain.nii.gz --reg /home/tylers/bbreg_test/init-fsl/fsl_register.dat --surf