Logfile for bbregister dom oct 16 01:04:59 CEST 2011 setenv SUBJECTS_DIR /home/joana/subjects cd /home/joana/Desktop/BEFREE/CN21 /usr/local/freesurfer5/freesurfer/bin/bbregister --s H_CN21 --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_CN21 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25146/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.25146/fslregister --dof 6 Log file is ./tmp.bbregister.25146/reg.init.dat.fslregister.log dom oct 16 01:05:00 CEST 2011 --s H_CN21 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25146/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.25146/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/CN21 mri_convert /home/joana/subjects/H_CN21/mri/brainmask.mgz ./tmp.bbregister.25146/fslregister/refvol.fslregister.nii mri_convert /home/joana/subjects/H_CN21/mri/brainmask.mgz ./tmp.bbregister.25146/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_CN21/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, -5.96046e-08) writing to ./tmp.bbregister.25146/fslregister/refvol.fslregister.nii... -------------------------------------- /home/joana/Desktop/BEFREE/CN21 mri_convert template_bbregister.nii.gz ./tmp.bbregister.25146/fslregister/movvol.fslregister.nii --frame 0 mri_convert template_bbregister.nii.gz ./tmp.bbregister.25146/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.25146/fslregister/movvol.fslregister.nii... Mov determinant is -10.9178 /home/joana/Desktop/BEFREE/CN21 tkregister2_cmdl --mov ./tmp.bbregister.25146/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.25146/fslregister/reg0.25187.dat --regheader --fslregout ./tmp.bbregister.25146/reg.init.dat.fsl.mat0 --s H_CN21 --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.25146/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.25146/fslregister/reg0.25187.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_CN21/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.25146/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 -126.500; 0.000 -0.000 1.000 -47.170; 0.000 -1.000 0.000 125.275; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 0.000 -126.500; 0.000 -0.000 1.000 -47.170; 0.000 -1.000 0.000 125.275; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN21 RegMat --------------------------- 1.000 0.000 0.000 -126.500; 0.000 -0.000 1.000 -47.170; 0.000 -1.000 0.000 125.275; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -10.9178, ref det = -1 dom oct 16 01:05:03 CEST 2011 /home/joana/Desktop/BEFREE/CN21 flirt.fsl -ref ./tmp.bbregister.25146/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.25146/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.25146/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl-4.1.6//etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.25146/reg.init.dat.fsl.mat0 dom oct 16 01:05:12 CEST 2011 /home/joana/Desktop/BEFREE/CN21 flirt.fsl -ref ./tmp.bbregister.25146/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.25146/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.25146/reg.init.dat.fsl.mat -init ./tmp.bbregister.25146/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer5/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s H_CN21 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25146/reg.init.dat --fslreg ./tmp.bbregister.25146/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer5/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.890 -0.167 -0.425 52.307; -0.319 0.440 -0.840 157.987; 0.327 0.882 0.338 -45.206; 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.25146/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_CN21/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) -------- 0.890 -0.327 -0.319 -8.559; 0.425 0.338 0.840 -5.672; -0.167 -0.882 0.440 -2.027; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.890 -0.327 -0.319 -8.559; 0.425 0.338 0.840 -5.672; -0.167 -0.882 0.440 -2.027; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = H_CN21 RegMat --------------------------- 0.890 -0.327 -0.319 -8.559; 0.425 0.338 0.840 -5.672; -0.167 -0.882 0.440 -2.027; 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 01:05:00 CEST 2011 Ended at dom oct 16 01:05:27 CEST 2011 fslregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.25146/reg.init.dat --surf orig mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25146/reg.init.dat --out-reg ./tmp.bbregister.25146/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/CN21 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25146/reg.init.dat --out-reg ./tmp.bbregister.25146/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.25146/reg.init.dat subject H_CN21 dof 6 outregfile ./tmp.bbregister.25146/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 1319153466 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.890 -0.327 -0.319 -8.559; 0.425 0.338 0.840 -5.672; -0.167 -0.882 0.440 -2.027; 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 1.004119 1 -25.0 -25.0 25.0 1.012515 2 -25.0 25.0 -25.0 1.008709 3 -25.0 25.0 25.0 1.009233 4 25.0 -25.0 -25.0 1.029737 5 25.0 -25.0 25.0 0.976772 6 25.0 25.0 -25.0 1.014213 7 25.0 25.0 25.0 1.009480 REL: 8 0.955481 8.064778 1.008097 rel = 0.947807 Initial costs ---------------- Number of surface hits 2494 WM Intensity 600.1648 +/- 279.3152 Ctx Intensity 595.8900 +/- 280.8061 Pct Contrast -1.5524 +/- 37.6663 Cost 0.9555 RelCost 0.9478 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 0.9894 0.9894 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9855 0.9855 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9736 0.9736 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9528 0.9528 0.0 264 0.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.9516 0.9516 0.0 279 0.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.9465 0.9465 0.0 390 0.0000 0.0000 4.0000 0.0000 0.0000 -4.0000 0.9414 0.9414 0.0 396 0.0000 0.0000 4.0000 4.0000 -4.0000 -4.0000 0.9357 0.9357 0.0 Brute Force -------------------------- Min cost was 0.935666 Number of iterations 729 Search time 2.278000 sec Parameters at best (transmm, rotdeg) 0.000 0.000 4.000 4.000 -4.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 4 3 4 4 -4 5 -4 6 0.382 0.000 4.000 4.000 -4.000 -4.000 0.9276953838 13 0.382 1.000 4.000 4.000 -4.000 -4.000 0.9173996802 20 0.382 1.090 4.000 4.000 -4.000 -4.000 0.9169831939 31 0.382 1.090 4.382 4.000 -4.000 -4.000 0.9137603937 35 0.382 1.090 4.386 4.000 -4.000 -4.000 0.9137543889 43 0.382 1.090 4.386 3.382 -4.000 -4.000 0.8981420162 45 0.382 1.090 4.386 3.549 -4.000 -4.000 0.8974763537 46 0.382 1.090 4.386 3.496 -4.000 -4.000 0.8970764904 48 0.382 1.090 4.386 3.504 -4.000 -4.000 0.8970278834 50 0.382 1.090 4.386 3.510 -4.000 -4.000 0.8969906035 51 0.382 1.090 4.386 3.514 -4.000 -4.000 0.8969692419 52 0.382 1.090 4.386 3.517 -4.000 -4.000 0.8969580475 73 0.382 1.090 4.386 3.517 -4.000 -4.179 0.8948136096 74 0.382 1.090 4.386 3.517 -4.000 -4.180 0.8943671485 77 0.382 1.090 4.386 3.517 -4.000 -4.212 0.8940143725 78 0.382 1.090 4.386 3.517 -4.000 -4.211 0.8940096910 79 0.382 1.090 4.386 3.517 -4.000 -4.206 0.8939939554 92 0.400 1.090 4.386 3.517 -4.000 -4.206 0.8932638073 96 0.404 1.090 4.386 3.517 -4.000 -4.206 0.8931443015 99 0.405 1.090 4.386 3.517 -4.000 -4.206 0.8931247022 107 0.405 1.051 4.386 3.517 -4.000 -4.206 0.8928132169 108 0.405 1.049 4.386 3.517 -4.000 -4.206 0.8927953919 109 0.405 1.029 4.386 3.517 -4.000 -4.206 0.8927477539 110 0.405 1.035 4.386 3.517 -4.000 -4.206 0.8927343408 120 0.405 1.035 4.434 3.517 -4.000 -4.206 0.8926369278 121 0.405 1.035 4.415 3.517 -4.000 -4.206 0.8925881774 122 0.405 1.035 4.416 3.517 -4.000 -4.206 0.8925856246 123 0.405 1.035 4.419 3.517 -4.000 -4.206 0.8925839797 132 0.405 1.035 4.419 3.478 -4.000 -4.206 0.8922276693 138 0.405 1.035 4.419 3.477 -4.000 -4.206 0.8922215040 146 0.405 1.035 4.419 3.477 -3.982 -4.206 0.8921592030 147 0.405 1.035 4.419 3.477 -3.974 -4.206 0.8919963026 150 0.405 1.035 4.419 3.477 -3.950 -4.206 0.8919711606 152 0.405 1.035 4.419 3.477 -3.939 -4.206 0.8917556955 155 0.405 1.035 4.419 3.477 -3.936 -4.206 0.8916833150 156 0.405 1.035 4.419 3.477 -3.935 -4.206 0.8916458483 164 0.405 1.035 4.419 3.477 -3.935 -4.304 0.8914994775 169 0.405 1.035 4.419 3.477 -3.935 -4.296 0.8914120141 170 0.405 1.035 4.419 3.477 -3.935 -4.287 0.8913370376 171 0.405 1.035 4.419 3.477 -3.935 -4.278 0.8912907228 172 0.405 1.035 4.419 3.477 -3.935 -4.272 0.8912697734 173 0.405 1.035 4.419 3.477 -3.935 -4.269 0.8912591253 174 0.405 1.035 4.419 3.477 -3.935 -4.267 0.8912537883 186 0.396 1.035 4.419 3.477 -3.935 -4.267 0.8911592174 187 0.376 1.035 4.419 3.477 -3.935 -4.267 0.8911109342 188 0.381 1.035 4.419 3.477 -3.935 -4.267 0.8910980289 190 0.380 1.035 4.419 3.477 -3.935 -4.267 0.8910972318 191 0.379 1.035 4.419 3.477 -3.935 -4.267 0.8910949651 200 0.379 1.098 4.419 3.477 -3.935 -4.267 0.8910401904 201 0.379 1.068 4.419 3.477 -3.935 -4.267 0.8909534087 226 0.379 1.068 4.419 3.463 -3.935 -4.267 0.8908180224 228 0.379 1.068 4.419 3.445 -3.935 -4.267 0.8905740501 231 0.379 1.068 4.419 3.441 -3.935 -4.267 0.8905335733 232 0.379 1.068 4.419 3.438 -3.935 -4.267 0.8905161830 233 0.379 1.068 4.419 3.436 -3.935 -4.267 0.8905080602 234 0.379 1.068 4.419 3.435 -3.935 -4.267 0.8905040590 248 0.379 1.068 4.419 3.435 -3.934 -4.267 0.8904858371 257 0.379 1.068 4.419 3.435 -3.934 -4.263 0.8904799770 258 0.379 1.068 4.419 3.435 -3.934 -4.262 0.8904796116 271 0.385 1.068 4.419 3.435 -3.934 -4.262 0.8904559948 282 0.385 1.070 4.419 3.435 -3.934 -4.262 0.8904511011 283 0.385 1.072 4.419 3.435 -3.934 -4.262 0.8904488324 296 0.385 1.072 4.413 3.435 -3.934 -4.262 0.8904415215 297 0.385 1.072 4.414 3.435 -3.934 -4.262 0.8904412205 310 0.385 1.072 4.414 3.433 -3.934 -4.262 0.8904316859 311 0.385 1.072 4.414 3.432 -3.934 -4.262 0.8904273050 312 0.385 1.072 4.414 3.431 -3.934 -4.262 0.8904247999 327 0.385 1.072 4.414 3.431 -3.933 -4.262 0.8904106852 337 0.385 1.072 4.414 3.431 -3.933 -4.260 0.8904092740 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 0.986114 1 -25.0 -25.0 25.0 0.994925 2 -25.0 25.0 -25.0 1.022539 3 -25.0 25.0 25.0 1.029381 4 25.0 -25.0 -25.0 1.009933 5 25.0 -25.0 25.0 1.001905 6 25.0 25.0 -25.0 0.991381 7 25.0 25.0 25.0 1.023714 REL: 8 0.890409 8.059890 1.007486 rel = 0.883793 Number of iterations 3 Min cost was 0.890409 Number of FunctionCalls 340 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.056000 sec Parameters at optimum (transmm) 0.38513 1.07207 4.41409 Parameters at optimum (rotdeg) 3.43090 -3.93257 -4.25984 Final costs ---------------- Number of surface hits 2486 WM Intensity 596.0812 +/- 276.0419 Ctx Intensity 602.5502 +/- 287.0814 Pct Contrast -0.3999 +/- 39.4123 Cost 0.8904 RelCost 0.9478 Reg at min cost was 0.927 -0.238 -0.290 -8.380; 0.367 0.409 0.836 -3.831; -0.080 -0.881 0.466 1.470; 0.000 0.000 0.000 1.000; Writing optimal reg to ./tmp.bbregister.25146/bbr.pass1.dat, type = 14 Original Reg 0.890 -0.327 -0.319 -8.559; 0.425 0.338 0.840 -5.672; -0.167 -0.882 0.440 -2.027; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.037 -0.090 -0.028 -0.179; 0.059 -0.071 0.004 -1.841; -0.087 -0.001 -0.026 -3.497; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 5.793214 Computing change in rh position Surface RMS Diff (mm) 6.793386 11.399654 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.25146/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.25146/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/CN21 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.25146/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.25146/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.25146/bbr.pass1.dat subject H_CN21 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 1319612927 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.927 -0.238 -0.290 -8.380; 0.367 0.409 0.836 -3.831; -0.080 -0.881 0.466 1.470; 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 0.978523 1 -25.0 -25.0 25.0 1.015631 2 -25.0 25.0 -25.0 1.034607 3 -25.0 25.0 25.0 1.020485 4 25.0 -25.0 -25.0 1.015176 5 25.0 -25.0 25.0 1.012865 6 25.0 25.0 -25.0 1.039842 7 25.0 25.0 25.0 1.018593 REL: 8 0.975491 8.135721 1.016965 rel = 0.959218 Initial costs ---------------- Number of surface hits 250983 WM Intensity 604.1886 +/- 280.4921 Ctx Intensity 604.2548 +/- 290.5027 Pct Contrast -1.3425 +/- 39.0289 Cost 0.9755 RelCost 0.9592 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 -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9097 0.9097 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.9066 0.9066 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.9046 0.9046 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.9009 0.9009 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8997 0.8997 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8983 0.8983 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.8974 0.8974 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.8972 0.8972 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.8948 0.8948 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.8946 0.8946 0.0 96 -0.1000 0.0000 -0.1000 0.0000 0.1000 -0.1000 0.8929 0.8929 0.0 105 -0.1000 0.0000 -0.1000 0.1000 0.1000 -0.1000 0.8924 0.8924 0.0 106 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.0000 0.8919 0.8919 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8904 0.8904 0.0 Brute Force -------------------------- Min cost was 0.890409 Number of iterations 729 Search time 2.227000 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 7 -0.138 0.000 0.000 0.000 0.000 0.000 0.9751443055 10 -0.147 0.000 0.000 0.000 0.000 0.000 0.9751287150 11 -0.167 0.000 0.000 0.000 0.000 0.000 0.9751265859 12 -0.158 0.000 0.000 0.000 0.000 0.000 0.9751247191 15 -0.157 0.000 0.000 0.000 0.000 0.000 0.9751238290 16 -0.156 0.000 0.000 0.000 0.000 0.000 0.9751231582 21 -0.156 -0.618 0.000 0.000 0.000 0.000 0.9734614525 24 -0.156 -0.695 0.000 0.000 0.000 0.000 0.9733561830 26 -0.156 -0.709 0.000 0.000 0.000 0.000 0.9733521220 28 -0.156 -0.708 0.000 0.000 0.000 0.000 0.9733476370 29 -0.156 -0.703 0.000 0.000 0.000 0.000 0.9733444080 30 -0.156 -0.705 0.000 0.000 0.000 0.000 0.9733390072 34 -0.156 -0.705 -1.618 0.000 0.000 0.000 0.9714279712 37 -0.156 -0.705 -1.000 0.000 0.000 0.000 0.9713596793 39 -0.156 -0.705 -1.285 0.000 0.000 0.000 0.9712658481 40 -0.156 -0.705 -1.267 0.000 0.000 0.000 0.9712530240 44 -0.156 -0.705 -1.274 0.000 0.000 0.000 0.9712529824 45 -0.156 -0.705 -1.271 0.000 0.000 0.000 0.9712508619 46 -0.156 -0.705 -1.270 0.000 0.000 0.000 0.9712501674 47 -0.156 -0.705 -1.269 0.000 0.000 0.000 0.9712495605 49 -0.156 -0.705 -1.269 1.000 0.000 0.000 0.9628838730 50 -0.156 -0.705 -1.269 2.618 0.000 0.000 0.9577366810 54 -0.156 -0.705 -1.269 3.618 0.000 0.000 0.9568038996 56 -0.156 -0.705 -1.269 3.235 0.000 0.000 0.9566189390 59 -0.156 -0.705 -1.269 3.145 0.000 0.000 0.9566031388 64 -0.156 -0.705 -1.269 3.137 0.000 0.000 0.9565968101 66 -0.156 -0.705 -1.269 3.139 0.000 0.000 0.9565909642 72 -0.156 -0.705 -1.269 3.139 -0.618 0.000 0.9560274359 74 -0.156 -0.705 -1.269 3.139 -0.567 0.000 0.9559724693 76 -0.156 -0.705 -1.269 3.139 -0.516 0.000 0.9559467542 77 -0.156 -0.705 -1.269 3.139 -0.495 0.000 0.9558683261 78 -0.156 -0.705 -1.269 3.139 -0.440 0.000 0.9558451362 79 -0.156 -0.705 -1.269 3.139 -0.462 0.000 0.9557800913 80 -0.156 -0.705 -1.269 3.139 -0.465 0.000 0.9557786183 84 -0.156 -0.705 -1.269 3.139 -0.465 1.000 0.9540082500 87 -0.156 -0.705 -1.269 3.139 -0.465 1.618 0.9524551906 94 -0.156 -0.705 -1.269 3.139 -0.465 1.613 0.9524476818 105 0.226 -0.705 -1.269 3.139 -0.465 1.613 0.9519557753 109 0.169 -0.705 -1.269 3.139 -0.465 1.613 0.9519075266 111 0.158 -0.705 -1.269 3.139 -0.465 1.613 0.9519007752 115 0.162 -0.705 -1.269 3.139 -0.465 1.613 0.9518936065 117 0.163 -0.705 -1.269 3.139 -0.465 1.613 0.9518930823 125 0.163 -0.722 -1.269 3.139 -0.465 1.613 0.9518173972 126 0.163 -0.801 -1.269 3.139 -0.465 1.613 0.9516284677 128 0.163 -0.789 -1.269 3.139 -0.465 1.613 0.9516239838 133 0.163 -0.788 -1.269 3.139 -0.465 1.613 0.9516227199 134 0.163 -0.787 -1.269 3.139 -0.465 1.613 0.9516219886 137 0.163 -0.787 -0.269 3.139 -0.465 1.613 0.9513062803 146 0.163 -0.787 -0.268 3.139 -0.465 1.613 0.9513062269 160 0.163 -0.787 -0.268 3.141 -0.465 1.613 0.9513055459 170 0.163 -0.787 -0.268 3.141 -0.345 1.613 0.9512028458 174 0.163 -0.787 -0.268 3.141 -0.352 1.613 0.9511957549 175 0.163 -0.787 -0.268 3.141 -0.359 1.613 0.9511944068 176 0.163 -0.787 -0.268 3.141 -0.357 1.613 0.9511929699 177 0.163 -0.787 -0.268 3.141 -0.356 1.613 0.9511884871 186 0.163 -0.787 -0.268 3.141 -0.356 1.586 0.9511594204 188 0.163 -0.787 -0.268 3.141 -0.356 1.587 0.9511554717 201 0.193 -0.787 -0.268 3.141 -0.356 1.587 0.9511225202 203 0.185 -0.787 -0.268 3.141 -0.356 1.587 0.9511211364 204 0.188 -0.787 -0.268 3.141 -0.356 1.587 0.9511205590 213 0.188 -1.016 -0.268 3.141 -0.356 1.587 0.9504628890 214 0.188 -1.029 -0.268 3.141 -0.356 1.587 0.9504612009 215 0.188 -1.028 -0.268 3.141 -0.356 1.587 0.9504592742 223 0.188 -1.028 0.114 3.141 -0.356 1.587 0.9501083350 228 0.188 -1.028 0.149 3.141 -0.356 1.587 0.9500632980 235 0.188 -1.028 0.145 3.141 -0.356 1.587 0.9500616124 242 0.188 -1.028 0.145 3.256 -0.356 1.587 0.9499803162 243 0.188 -1.028 0.145 3.247 -0.356 1.587 0.9499725152 244 0.188 -1.028 0.145 3.222 -0.356 1.587 0.9499660272 246 0.188 -1.028 0.145 3.227 -0.356 1.587 0.9499532919 249 0.188 -1.028 0.145 3.226 -0.356 1.587 0.9499517034 252 0.188 -1.028 0.145 3.226 0.644 1.587 0.9492760342 258 0.188 -1.028 0.145 3.226 0.498 1.587 0.9492665092 259 0.188 -1.028 0.145 3.226 0.461 1.587 0.9491408766 263 0.188 -1.028 0.145 3.226 0.450 1.587 0.9491362141 264 0.188 -1.028 0.145 3.226 0.451 1.587 0.9491347912 266 0.188 -1.028 0.145 3.226 0.452 1.587 0.9491290681 267 0.188 -1.028 0.145 3.226 0.453 1.587 0.9491277866 274 0.188 -1.028 0.145 3.226 0.453 1.458 0.9490833613 275 0.188 -1.028 0.145 3.226 0.453 1.486 0.9490661041 276 0.188 -1.028 0.145 3.226 0.453 1.505 0.9490576134 281 0.188 -1.028 0.145 3.226 0.453 1.506 0.9490575117 282 0.213 -1.269 0.557 3.311 1.263 1.424 0.9482714418 293 0.213 -1.269 0.558 3.312 1.263 1.424 0.9482674087 307 0.202 -1.269 0.558 3.312 1.263 1.424 0.9482584616 317 0.202 -1.242 0.558 3.312 1.263 1.424 0.9482501519 318 0.202 -1.241 0.558 3.312 1.263 1.424 0.9482469141 331 0.202 -1.241 0.595 3.312 1.263 1.424 0.9481796454 334 0.202 -1.241 0.600 3.312 1.263 1.424 0.9481780685 343 0.202 -1.241 0.600 3.218 1.263 1.424 0.9481431666 344 0.202 -1.241 0.600 3.237 1.263 1.424 0.9481356116 345 0.202 -1.241 0.600 3.246 1.263 1.424 0.9481336414 346 0.202 -1.241 0.600 3.271 1.263 1.424 0.9481224786 347 0.202 -1.241 0.600 3.287 1.263 1.424 0.9481073526 392 0.027 -1.241 0.600 3.287 1.263 1.424 0.9481015529 393 0.111 -1.241 0.600 3.287 1.263 1.424 0.9480918250 394 0.104 -1.241 0.600 3.287 1.263 1.424 0.9480911336 395 0.090 -1.241 0.600 3.287 1.263 1.424 0.9480764799 399 0.087 -1.241 0.600 3.287 1.263 1.424 0.9480706128 408 0.087 -1.262 0.600 3.287 1.263 1.424 0.9480683172 412 0.087 -1.295 0.600 3.287 1.263 1.424 0.9480322610 414 0.087 -1.294 0.600 3.287 1.263 1.424 0.9480234789 417 0.087 -1.292 0.600 3.287 1.263 1.424 0.9480171950 419 0.087 -1.293 0.600 3.287 1.263 1.424 0.9480111515 426 0.087 -1.293 0.646 3.287 1.263 1.424 0.9478284574 429 0.087 -1.293 0.653 3.287 1.263 1.424 0.9478264368 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.979294 1 -25.0 -25.0 25.0 1.033292 2 -25.0 25.0 -25.0 1.037740 3 -25.0 25.0 25.0 1.018136 4 25.0 -25.0 -25.0 1.021454 5 25.0 -25.0 25.0 0.992989 6 25.0 25.0 -25.0 1.010974 7 25.0 25.0 25.0 0.993546 REL: 8 0.947826 8.087425 1.010928 rel = 0.93758 Number of iterations 5 Min cost was 0.947826 Number of FunctionCalls 567 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 87.991000 sec Parameters at optimum (transmm) 0.08709 -1.29272 0.65328 Parameters at optimum (rotdeg) 3.28664 1.26337 1.42405 Final costs ---------------- Number of surface hits 244314 WM Intensity 589.0162 +/- 273.8422 Ctx Intensity 595.4757 +/- 280.5824 Pct Contrast 0.1655 +/- 37.7973 Cost 0.9478 RelCost 0.9592 Reg at min cost was 0.916 -0.268 -0.299 -8.163; 0.393 0.452 0.800 -5.408; -0.079 -0.851 0.520 2.085; 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 0.927 -0.238 -0.290 -8.380; 0.367 0.409 0.836 -3.831; -0.080 -0.881 0.466 1.470; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.011 0.030 0.009 -0.216; -0.027 -0.043 0.035 1.577; -0.001 -0.030 -0.053 -0.616; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 4.424062 Computing change in rh position Surface RMS Diff (mm) 3.857279 7.883232 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 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 -------- 0.916 -0.268 -0.299 -8.163; 0.393 0.452 0.800 -5.408; -0.079 -0.851 0.520 2.085; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/joana/subjects/H_CN21/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 -------- 0.916 -0.268 -0.299 -8.163; 0.393 0.452 0.800 -5.408; -0.079 -0.851 0.520 2.085; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN21 RegMat --------------------------- 0.916 -0.268 -0.299 -8.163; 0.393 0.452 0.800 -5.408; -0.079 -0.851 0.520 2.085; 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 01:04:59 CEST 2011 Ended at dom oct 16 01:07:29 CEST 2011 BBR-Run-Time-Sec 150 bbregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg register.dat --surf