Logfile for bbregister dom oct 16 01:21:24 CEST 2011 setenv SUBJECTS_DIR /home/joana/subjects cd /home/joana/Desktop/BEFREE/CN23 /usr/local/freesurfer5/freesurfer/bin/bbregister --s H_CN23 --mov nodif_brain.nii.gz --reg register.dat --init-fsl --dti --template-out template_bbregister.nii.gz --fslmat flirt.tmx --o output_bbregister.nii.gz $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ub029113 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer5/freesurfer mri_convert nodif_brain.nii.gz template_bbregister.nii.gz mri_convert nodif_brain.nii.gz template_bbregister.nii.gz WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from nodif_brain.nii.gz... TR=100000000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to template_bbregister.nii.gz... fslregister --s H_CN23 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25944/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.25944/fslregister --dof 6 Log file is ./tmp.bbregister.25944/reg.init.dat.fslregister.log dom oct 16 01:21:25 CEST 2011 --s H_CN23 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25944/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.25944/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ub029113 Linux ub029113 2.6.18-164.11.1.el5 #1 SMP Wed Jan 6 13:26:04 EST 2010 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/joana/Desktop/BEFREE/CN23 mri_convert /home/joana/subjects/H_CN23/mri/brainmask.mgz ./tmp.bbregister.25944/fslregister/refvol.fslregister.nii mri_convert /home/joana/subjects/H_CN23/mri/brainmask.mgz ./tmp.bbregister.25944/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/joana/subjects/H_CN23/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (5.55111e-17, 1.19209e-07, -1) k_ras = (-1.11022e-16, 1, -7.10543e-15) writing to ./tmp.bbregister.25944/fslregister/refvol.fslregister.nii... -------------------------------------- /home/joana/Desktop/BEFREE/CN23 mri_convert template_bbregister.nii.gz ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii --frame 0 mri_convert template_bbregister.nii.gz ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from template_bbregister.nii.gz... TR=100000000.00, 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 ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii... Mov determinant is -10.9178 /home/joana/Desktop/BEFREE/CN23 tkregister2_cmdl --mov ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.25944/fslregister/reg0.25982.dat --regheader --fslregout ./tmp.bbregister.25944/reg.init.dat.fsl.mat0 --s H_CN23 --noedit tkregister_tcl /usr/local/freesurfer5/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.25944/fslregister/reg0.25982.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/joana/subjects/H_CN23/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 ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.049 0.000 0.000 125.000; 0.000 0.000 2.600 -57.200; 0.000 -2.049 0.000 125.000; 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 -125.210; 0.000 -0.000 1.000 -53.776; 0.000 -1.000 0.000 117.037; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -125.210; 0.000 -0.000 1.000 -53.776; 0.000 -1.000 0.000 117.037; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN23 RegMat --------------------------- 1.000 0.000 0.000 -125.210; 0.000 -0.000 1.000 -53.776; 0.000 -1.000 0.000 117.037; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -10.9178, ref det = -1 dom oct 16 01:21:32 CEST 2011 /home/joana/Desktop/BEFREE/CN23 flirt.fsl -ref ./tmp.bbregister.25944/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.25944/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl-4.1.6//etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.25944/reg.init.dat.fsl.mat0 dom oct 16 01:21:41 CEST 2011 /home/joana/Desktop/BEFREE/CN23 flirt.fsl -ref ./tmp.bbregister.25944/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.25944/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.25944/reg.init.dat.fsl.mat -init ./tmp.bbregister.25944/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer5/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s H_CN23 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25944/reg.init.dat --fslreg ./tmp.bbregister.25944/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer5/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.840 -0.265 0.474 36.016; 0.538 0.286 -0.793 57.721; 0.075 0.921 0.382 -28.810; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume template_bbregister.nii.gz reg file ./tmp.bbregister.25944/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /home/joana/subjects/H_CN23/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 template_bbregister.nii.gz Tmov: -------------------- -2.049 0.000 0.000 125.000; 0.000 0.000 2.600 -57.200; 0.000 -2.049 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -10.9178, ref det = -1 ---- Input registration matrix (computed) -------- 0.840 -0.075 0.538 -1.753; -0.474 0.382 0.793 -9.401; -0.265 -0.921 0.286 -15.138; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.840 -0.075 0.538 -1.753; -0.474 0.382 0.793 -9.401; -0.265 -0.921 0.286 -15.138; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN23 RegMat --------------------------- 0.840 -0.075 0.538 -1.753; -0.474 0.382 0.793 -9.401; -0.265 -0.921 0.286 -15.138; 0.000 0.000 0.000 1.000; (standard_in) 1: illegal character: H (standard_in) 1: illegal character: _ (standard_in) 1: illegal character: N (standard_in) 1: parse error Started at dom oct 16 01:21:25 CEST 2011 Ended at dom oct 16 01:21:55 CEST 2011 fslregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25944/reg.init.dat --surf orig mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25944/reg.init.dat --out-reg ./tmp.bbregister.25944/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /home/joana/subjects cd /home/joana/Desktop/BEFREE/CN23 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25944/reg.init.dat --out-reg ./tmp.bbregister.25944/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 sysname Linux hostname ub029113 machine x86_64 user joana movvol template_bbregister.nii.gz regfile ./tmp.bbregister.25944/reg.init.dat subject H_CN23 dof 6 outregfile ./tmp.bbregister.25944/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 TolPowell 0.000100 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1319010711 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.840 -0.075 0.538 -1.753; -0.474 0.382 0.793 -9.401; -0.265 -0.921 0.286 -15.138; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 0.997896 1 -25.0 -25.0 25.0 1.044817 2 -25.0 25.0 -25.0 0.998652 3 -25.0 25.0 25.0 1.014886 4 25.0 -25.0 -25.0 0.984349 5 25.0 -25.0 25.0 0.984554 6 25.0 25.0 -25.0 0.988044 7 25.0 25.0 25.0 1.073447 REL: 8 0.992969 8.086643 1.010830 rel = 0.98233 Initial costs ---------------- Number of surface hits 2626 WM Intensity 624.1183 +/- 270.2288 Ctx Intensity 623.3588 +/- 280.7421 Pct Contrast -2.1212 +/- 38.0312 Cost 0.9930 RelCost 0.9823 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0127 1.0127 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9925 0.9925 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9698 0.9698 0.0 11 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.9290 0.9290 0.0 245 0.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9245 0.9245 0.0 Brute Force -------------------------- Min cost was 0.924549 Number of iterations 729 Search time 2.479000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 -4.000 -4.000 -4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 -4 3 -4 4 -4 5 4 2 1.000 -4.000 -4.000 -4.000 -4.000 4.000 0.9218562108 6 0.618 -4.000 -4.000 -4.000 -4.000 4.000 0.9176848103 8 0.718 -4.000 -4.000 -4.000 -4.000 4.000 0.9145400356 9 0.826 -4.000 -4.000 -4.000 -4.000 4.000 0.9140301818 10 0.790 -4.000 -4.000 -4.000 -4.000 4.000 0.9138160054 12 0.797 -4.000 -4.000 -4.000 -4.000 4.000 0.9138091882 14 0.795 -4.000 -4.000 -4.000 -4.000 4.000 0.9138085998 16 0.796 -4.000 -4.000 -4.000 -4.000 4.000 0.9138085761 24 0.796 -4.026 -4.000 -4.000 -4.000 4.000 0.9134889803 25 0.796 -4.040 -4.000 -4.000 -4.000 4.000 0.9132967366 26 0.796 -4.058 -4.000 -4.000 -4.000 4.000 0.9132923344 27 0.796 -4.049 -4.000 -4.000 -4.000 4.000 0.9132419805 29 0.796 -4.050 -4.000 -4.000 -4.000 4.000 0.9132414543 40 0.796 -4.050 -4.090 -4.000 -4.000 4.000 0.9132159185 41 0.796 -4.050 -4.046 -4.000 -4.000 4.000 0.9129285832 43 0.796 -4.050 -4.054 -4.000 -4.000 4.000 0.9129020006 44 0.796 -4.050 -4.068 -4.000 -4.000 4.000 0.9128752094 46 0.796 -4.050 -4.067 -4.000 -4.000 4.000 0.9128678447 47 0.796 -4.050 -4.062 -4.000 -4.000 4.000 0.9124885584 50 0.796 -4.050 -4.061 -4.000 -4.000 4.000 0.9124853291 72 0.796 -4.050 -4.061 -4.000 -4.019 4.000 0.9124654226 76 0.796 -4.050 -4.061 -4.000 -4.029 4.000 0.9123331920 77 0.796 -4.050 -4.061 -4.000 -4.035 4.000 0.9122888727 81 0.796 -4.050 -4.061 -4.000 -4.036 4.000 0.9122849684 88 0.796 -4.050 -4.061 -4.000 -4.036 3.959 0.9121338243 90 0.796 -4.050 -4.061 -4.000 -4.036 3.975 0.9120844091 91 0.796 -4.050 -4.061 -4.000 -4.036 3.972 0.9120838045 93 0.796 -4.050 -4.061 -4.000 -4.036 3.973 0.9120836092 103 0.785 -4.050 -4.061 -4.000 -4.036 3.973 0.9120804273 104 0.790 -4.050 -4.061 -4.000 -4.036 3.973 0.9120553510 157 0.790 -4.050 -4.061 -4.000 -4.032 3.973 0.9120487205 169 0.790 -4.050 -4.061 -4.000 -4.032 3.970 0.9120336009 170 0.790 -4.050 -4.061 -4.000 -4.032 3.957 0.9120263200 171 0.790 -4.050 -4.061 -4.000 -4.032 3.962 0.9120194186 Powell done niters = 1 Computing relative cost 0 -25.0 -25.0 -25.0 1.049060 1 -25.0 -25.0 25.0 1.090145 2 -25.0 25.0 -25.0 1.018324 3 -25.0 25.0 25.0 1.051904 4 25.0 -25.0 -25.0 0.974887 5 25.0 -25.0 25.0 1.076792 6 25.0 25.0 -25.0 0.968730 7 25.0 25.0 25.0 1.093597 REL: 8 0.912019 8.323439 1.040430 rel = 0.876579 Number of iterations 1 Min cost was 0.912019 Number of FunctionCalls 174 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.638000 sec Parameters at optimum (transmm) 0.79012 -4.05020 -4.06072 Parameters at optimum (rotdeg) -4.00000 -4.03160 3.96201 Final costs ---------------- Number of surface hits 2583 WM Intensity 598.2556 +/- 257.8472 Ctx Intensity 614.0154 +/- 268.2804 Pct Contrast 1.4238 +/- 37.1806 Cost 0.9120 RelCost 0.9823 Reg at min cost was 0.886 -0.030 0.463 0.780; -0.431 0.316 0.845 -14.509; -0.172 -0.948 0.267 -18.593; 0.000 0.000 0.000 1.000; Writing optimal reg to ./tmp.bbregister.25944/bbr.pass1.dat, type = 14 Original Reg 0.840 -0.075 0.538 -1.753; -0.474 0.382 0.793 -9.401; -0.265 -0.921 0.286 -15.138; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.046 -0.045 0.075 -2.533; -0.043 0.066 -0.052 5.109; -0.093 0.027 0.019 3.456; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 7.628469 Computing change in rh position Surface RMS Diff (mm) 6.039813 13.367738 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25944/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.25944/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --o output_bbregister.nii.gz --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /home/joana/subjects cd /home/joana/Desktop/BEFREE/CN23 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25944/bbr.pass1.dat --out-reg register.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param --surf white --cur-reg ./tmp.bbregister.25944/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --o output_bbregister.nii.gz --gm-gt-wm 0.5 sysname Linux hostname ub029113 machine x86_64 user joana movvol template_bbregister.nii.gz regfile ./tmp.bbregister.25944/bbr.pass1.dat subject H_CN23 dof 6 outregfile register.dat outfile output_bbregister.nii.gz 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 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1319347658 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.886 -0.030 0.463 0.780; -0.431 0.316 0.845 -14.509; -0.172 -0.948 0.267 -18.593; 0.000 0.000 0.000 1.000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness Projecting RH Surfs Computing relative cost 0 -25.0 -25.0 -25.0 1.033972 1 -25.0 -25.0 25.0 1.059145 2 -25.0 25.0 -25.0 1.006728 3 -25.0 25.0 25.0 1.058223 4 25.0 -25.0 -25.0 1.026440 5 25.0 -25.0 25.0 1.032150 6 25.0 25.0 -25.0 1.009544 7 25.0 25.0 25.0 1.049427 REL: 8 0.959235 8.275629 1.034454 rel = 0.927287 Initial costs ---------------- Number of surface hits 259564 WM Intensity 598.9412 +/- 257.6783 Ctx Intensity 607.8199 +/- 268.6843 Pct Contrast 0.3548 +/- 36.8849 Cost 0.9592 RelCost 0.9273 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9227 0.9227 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9220 0.9220 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.9176 0.9176 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.9146 0.9146 0.0 8 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1000 0.9138 0.9138 0.0 35 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.9121 0.9121 0.0 44 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.1000 0.9121 0.9121 0.0 71 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.1000 0.9112 0.9112 0.0 Brute Force -------------------------- Min cost was 0.911161 Number of iterations 729 Search time 2.536000 sec Parameters at best (transmm, rotdeg) -0.100 -0.100 0.100 0.000 0.100 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 -0.1 2 0.1 3 0 4 0.1 5 0.1 3 -1.718 -0.100 0.100 0.000 0.100 0.100 0.9570914043 4 -1.029 -0.100 0.100 0.000 0.100 0.100 0.9568963335 7 -1.292 -0.100 0.100 0.000 0.100 0.100 0.9565352762 9 -1.334 -0.100 0.100 0.000 0.100 0.100 0.9564527764 10 -1.365 -0.100 0.100 0.000 0.100 0.100 0.9564090614 14 -1.370 -0.100 0.100 0.000 0.100 0.100 0.9564025634 16 -1.369 -0.100 0.100 0.000 0.100 0.100 0.9564020242 17 -1.368 -0.100 0.100 0.000 0.100 0.100 0.9564016330 20 -1.368 0.900 0.100 0.000 0.100 0.100 0.9520059112 25 -1.368 1.173 0.100 0.000 0.100 0.100 0.9514898854 26 -1.368 1.177 0.100 0.000 0.100 0.100 0.9514781624 27 -1.368 1.307 0.100 0.000 0.100 0.100 0.9514095738 31 -1.368 1.288 0.100 0.000 0.100 0.100 0.9513871963 34 -1.368 1.283 0.100 0.000 0.100 0.100 0.9513578698 36 -1.368 1.282 0.100 0.000 0.100 0.100 0.9513565817 39 -1.368 1.282 -1.518 0.000 0.100 0.100 0.9510806293 40 -1.368 1.282 -0.734 0.000 0.100 0.100 0.9494705347 43 -1.368 1.282 -1.034 0.000 0.100 0.100 0.9490662537 47 -1.368 1.282 -1.045 0.000 0.100 0.100 0.9490611889 48 -1.368 1.282 -1.052 0.000 0.100 0.100 0.9490585737 49 -1.368 1.282 -1.072 0.000 0.100 0.100 0.9490534973 51 -1.368 1.282 -1.080 0.000 0.100 0.100 0.9490496451 53 -1.368 1.282 -1.079 0.000 0.100 0.100 0.9490492826 54 -1.368 1.282 -1.078 0.000 0.100 0.100 0.9490470226 71 -1.368 1.282 -1.078 0.001 0.100 0.100 0.9490433915 82 -1.368 1.282 -1.078 0.001 0.067 0.100 0.9490134197 84 -1.368 1.282 -1.078 0.001 0.077 0.100 0.9490084490 88 -1.368 1.282 -1.078 0.001 0.078 0.100 0.9490078633 89 -1.368 1.282 -1.078 0.001 0.079 0.100 0.9490036527 112 -1.371 1.282 -1.078 0.001 0.079 0.100 0.9489902981 123 -1.371 0.664 -1.078 0.001 0.079 0.100 0.9482712013 128 -1.371 0.654 -1.078 0.001 0.079 0.100 0.9482648387 130 -1.371 0.634 -1.078 0.001 0.079 0.100 0.9482580619 132 -1.371 0.635 -1.078 0.001 0.079 0.100 0.9482485028 133 -1.371 0.642 -1.078 0.001 0.079 0.100 0.9482403838 135 -1.371 0.647 -1.078 0.001 0.079 0.100 0.9482379702 146 -1.371 0.647 -1.099 0.001 0.079 0.100 0.9482172089 147 -1.371 0.647 -1.105 0.001 0.079 0.100 0.9481997267 148 -1.371 0.647 -1.118 0.001 0.079 0.100 0.9481879390 149 -1.371 0.647 -1.117 0.001 0.079 0.100 0.9481852092 164 -1.371 0.647 -1.117 0.002 0.079 0.100 0.9481845865 180 -1.371 0.647 -1.117 0.002 0.077 0.100 0.9481823962 182 -1.371 0.647 -1.117 0.002 0.078 0.100 0.9481770778 190 -1.371 0.647 -1.117 0.002 0.078 0.220 0.9481317974 192 -1.371 0.647 -1.117 0.002 0.078 0.178 0.9481158738 204 -1.656 0.647 -1.117 0.002 0.078 0.178 0.9474969011 205 -1.652 0.647 -1.117 0.002 0.078 0.178 0.9474785642 206 -1.559 0.647 -1.117 0.002 0.078 0.178 0.9474591901 208 -1.603 0.647 -1.117 0.002 0.078 0.178 0.9473940868 209 -1.602 0.647 -1.117 0.002 0.078 0.178 0.9473906737 210 -1.588 0.647 -1.117 0.002 0.078 0.178 0.9473806237 212 -1.593 0.647 -1.117 0.002 0.078 0.178 0.9473775953 213 -1.592 0.647 -1.117 0.002 0.078 0.178 0.9473745886 223 -1.592 0.674 -1.117 0.002 0.078 0.178 0.9473219179 227 -1.592 0.673 -1.117 0.002 0.078 0.178 0.9473182612 264 -1.592 0.673 -1.117 0.002 -0.092 0.178 0.9471167995 269 -1.592 0.673 -1.117 0.002 -0.091 0.178 0.9471167120 277 -1.592 0.673 -1.117 0.002 -0.091 0.252 0.9469683271 281 -1.592 0.673 -1.117 0.002 -0.091 0.251 0.9469645573 296 -1.568 0.673 -1.117 0.002 -0.091 0.251 0.9469570896 297 -1.579 0.673 -1.117 0.002 -0.091 0.251 0.9469452478 299 -1.584 0.673 -1.117 0.002 -0.091 0.251 0.9469431777 300 -1.585 0.673 -1.117 0.002 -0.091 0.251 0.9469430715 310 -1.585 0.714 -1.117 0.002 -0.091 0.251 0.9469321022 311 -1.585 0.704 -1.117 0.002 -0.091 0.251 0.9468987985 313 -1.585 0.700 -1.117 0.002 -0.091 0.251 0.9468947158 322 -1.585 0.700 -1.110 0.002 -0.091 0.251 0.9468916682 324 -1.585 0.700 -1.109 0.002 -0.091 0.251 0.9468911224 327 -1.585 0.700 -1.108 0.002 -0.091 0.251 0.9468904632 328 -1.585 0.700 -1.107 0.002 -0.091 0.251 0.9468901637 335 -1.585 0.700 -1.107 -0.028 -0.091 0.251 0.9468732952 337 -1.585 0.700 -1.107 -0.025 -0.091 0.251 0.9468628079 340 -1.585 0.700 -1.107 -0.024 -0.091 0.251 0.9468497437 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.034821 1 -25.0 -25.0 25.0 1.038858 2 -25.0 25.0 -25.0 1.001300 3 -25.0 25.0 25.0 1.050319 4 25.0 -25.0 -25.0 1.031769 5 25.0 -25.0 25.0 1.033764 6 25.0 25.0 -25.0 0.997191 7 25.0 25.0 25.0 1.048531 REL: 8 0.946850 8.236552 1.029569 rel = 0.919656 Number of iterations 4 Min cost was 0.946850 Number of FunctionCalls 449 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 75.805000 sec Parameters at optimum (transmm) -1.58509 0.70021 -1.10704 Parameters at optimum (rotdeg) -0.02414 -0.09128 0.25132 Final costs ---------------- Number of surface hits 260727 WM Intensity 600.4946 +/- 256.5421 Ctx Intensity 610.8895 +/- 269.6791 Pct Contrast 0.7007 +/- 36.8442 Cost 0.9468 RelCost 0.9273 Reg at min cost was 0.888 -0.030 0.459 -0.712; -0.427 0.315 0.847 -13.813; -0.170 -0.949 0.267 -19.693; 0.000 0.000 0.000 1.000; Writing optimal reg to register.dat, type = 14 Writing output volume to output_bbregister.nii.gz Original Reg 0.886 -0.030 0.463 0.780; -0.431 0.316 0.845 -14.509; -0.172 -0.948 0.267 -18.593; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.002 -0.000 0.004 1.492; -0.004 0.001 -0.002 -0.696; -0.002 0.000 -0.000 1.100; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 2.079239 Computing change in rh position Surface RMS Diff (mm) 2.048795 2.271805 mri_segreg done tkregister2_cmdl --mov nodif_brain.nii.gz --reg register.dat --noedit --fslregout flirt.tmx tkregister_tcl /usr/local/freesurfer5/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume nodif_brain.nii.gz reg file register.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.888 -0.030 0.459 -0.712; -0.427 0.315 0.847 -13.813; -0.170 -0.949 0.267 -19.693; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/joana/subjects/H_CN23/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 nodif_brain.nii.gz Tmov: -------------------- -2.049 0.000 0.000 125.000; 0.000 0.000 2.600 -57.200; 0.000 -2.049 0.000 125.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.888 -0.030 0.459 -0.712; -0.427 0.315 0.847 -13.813; -0.170 -0.949 0.267 -19.693; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN23 RegMat --------------------------- 0.888 -0.030 0.459 -0.712; -0.427 0.315 0.847 -13.813; -0.170 -0.949 0.267 -19.693; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -10.9178, ref det = -1 Cleaning up Started at dom oct 16 01:21:24 CEST 2011 Ended at dom oct 16 01:23:48 CEST 2011 BBR-Run-Time-Sec 144 bbregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg register.dat --surf