Logfile for bbregister Fri Feb 12 11:31:49 MST 2016 setenv SUBJECTS_DIR /analysis/nihapoe_roi_nnn/Converter/FS_DIR cd 04_baseline/mri publicTool/free6surfer/freesurfer/bin/bbregister --s 10012004_baseline --mov baseline/crsummed_LIA.nii --init-fsl --t1 --lta output.lta $Id: bbregister,v 1.67.2.2 2015/09/21 19:40:00 greve Exp $ Linux paialv03 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME publicTool/free6surfer/freesurfer baseline/crsummed_LIA.nii ./tmp.bbregister.31499 /template.nii baseline/crsummed_LIA.nii ./tmp.bbregister.31499 /template.nii $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from ne/crsummed_LIA.nii... 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, 0) writing to ./tmp.bbregister.31499/template.nii... fslregister --s 10012004_baseline --mov ./tmp.bbregister.31499/template.nii --reg ./tmp.bbregister.31499/reg.init.dat --niters 1 --maxangle 90 --tmp ./tmp.bbregister.31499/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is ./tmp.bbregister.31499/reg.init.dat.fslregister.log Fri Feb 12 11:31:49 MST 2016 --s 10012004_baseline --mov ./tmp.bbregister.31499/template.nii --reg ./tmp.bbregister.31499/reg.init.dat --niters 1 - -maxangle 90 --tmp ./tmp.bbregister.31499/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov $Id: fslregister,v 1.39 2014/07/07 18:59:07 greve Exp $ paialv03 Linux paialv03 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- 04_baseline/mri mri_convert 04_baseline/mri/brainmask.mgz ./tmp.bbregister.31499/fslr egister/refvol.fslregister.nii mri_convert 04_baseline/mri/brainmask.mgz ./tmp.bbregister.31499/fslr egister/refvol.fslregister.nii $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from 04_baseline/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, 0) writing to ./tmp.bbregister.31499/fslregister/refvol.fslregister.nii... -------------------------------------- 04_baseline/mri mri_convert ./tmp.bbregister.31499/template.nii ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii --frame 0 mri_convert ./tmp.bbregister.31499/template.nii ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $ reading from ./tmp.bbregister.31499/template.nii... 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, 0) keeping frame 0 writing to ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii... Mov determinant is -1.43051 04_baseline/mri tkregister2_cmdl --mov ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.31499/fslregis ter/reg0.31535.dat --regheader --fslregout ./tmp.bbregister.31499/reg.init.dat.fsl.mat0 --s 10012004_baseline --noedit tkregister_tcl publicTool/free6surfer/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.31499/fslregister/reg0.31535.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 INFO: loading target 04_baseline/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable ./tmp.bbregister.31499/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.97656 0.00000 0.00000 93.75000; 0.00000 0.00000 1.50000 -108.00000; 0.00000 -0.97656 0.00000 125.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 1.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 1.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = 10012004_baseline RegMat --------------------------- 1.00000 0.00000 0.00000 -0.00002; 0.00000 1.00000 0.00000 -0.00002; 0.00000 0.00000 1.00000 0.00003; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1.43051, ref det = -1 Fri Feb 12 11:31:51 MST 2016 04_baseline/mri flirt.fsl -ref ./tmp.bbregister.31499/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.31499/fslregister/movvol .fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat . /tmp.bbregister.31499/fslregister/fslmat0.trans.mat -schedule publicTool/free6surfer/freesurfer/bin/ fsl.5.0.2.xyztrans.sch -init ./tmp.bbregister.31499/reg.init.dat.fsl.mat0 Fri Feb 12 11:32:35 MST 2016 04_baseline/mri flirt.fsl -ref ./tmp.bbregister.31499/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.31499/fslregister/movvol .fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat . /tmp.bbregister.31499/reg.init.dat.fsl.mat -init ./tmp.bbregister.31499/fslregister/fslmat0.trans.mat -schedule /apps/ banner/prod/publicTool/free6surfer/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s 10012004_baseline --mov ./tmp.bbregister.31499/template.nii --reg ./tmp.bbregister.31499/reg.init .dat --fslreg ./tmp.bbregister.31499/reg.init.dat.fsl.mat --noedit tkregister_tcl publicTool/free6surfer/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 1.00000 0.00089 0.00000 34.44450; -0.00089 1.00000 0.00000 3.12714; 0.00000 0.00000 1.00000 19.75310; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ./tmp.bbregister.31499/template.nii reg file ./tmp.bbregister.31499/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 INFO: loading target 04_baseline/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable ./tmp.bbregister.31499/template.nii Tmov: -------------------- -0.97656 0.00000 0.00000 93.75000; 0.00000 0.00000 1.50000 -108.00000; 0.00000 -0.97656 0.00000 125.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -1.43051, ref det = -1 ---- Input registration matrix (computed) -------- 1.00000 0.00000 -0.00089 0.30605; 0.00000 1.00000 0.00000 0.24690; 0.00089 0.00000 1.00000 0.04372; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 -0.00089 0.30605; 0.00000 1.00000 0.00000 0.24690; 0.00089 0.00000 1.00000 0.04372; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = 10012004_baseline RegMat --------------------------- 1.00000 0.00000 -0.00089 0.30605; 0.00000 1.00000 0.00000 0.24690; 0.00089 0.00000 1.00000 0.04372; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: _ (standard_in) 1: syntax error Started at Fri Feb 12 11:31:49 MST 2016 Ended at Fri Feb 12 11:33:23 MST 2016 fslregister Done To check results, run: tkregister2 --mov ./tmp.bbregister.31499/template.nii --reg ./tmp.bbregister.31499/reg.init.dat --surf orig mri_segreg --mov ./tmp.bbregister.31499/template.nii --init-reg ./tmp.bbregister.31499/reg.init.dat --out-reg ./tmp.bb register.31499/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --g m-proj-frac 0.5 --wm-gt-gm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /analysis/nihapoe_roi_nnn/Converter/FS_DIR cd 04_baseline/mri mri_segreg --mov ./tmp.bbregister.31499/template.nii --init-reg ./tmp.bbregister.31499/reg.init.dat --out-reg ./tmp.bb register.31499/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --g m-proj-frac 0.5 --wm-gt-gm 0.5 sysname Linux hostname paialv03 machine x86_64 user pthiyyagura movvol ./tmp.bbregister.31499/template.nii regfile ./tmp.bbregister.31499/reg.init.dat subject 10012004_baseline dof 6 outregfile ./tmp.bbregister.31499/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 1456280129 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.00000 0.00000 -0.00089 0.30605; 0.00000 1.00000 0.00000 0.24690; 0.00089 0.00000 1.00000 0.04372; 0.00000 0.00000 0.00000 1.00000; 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 for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.914728 1 -25.0 -25.0 25.0 0.921192 2 -25.0 25.0 -25.0 0.917316 3 -25.0 25.0 25.0 0.896277 4 25.0 -25.0 -25.0 0.930225 5 25.0 -25.0 25.0 0.955045 6 25.0 25.0 -25.0 0.935074 7 25.0 25.0 25.0 0.934066 REL: 8 0.960862 7.403922 0.925490 rel = 1.03822 Initial costs ---------------- Number of surface hits 2460 WM Intensity 0.0005 +/- 0.0002 Ctx Intensity 0.0005 +/- 0.0002 Pct Contrast -2.8667 +/- 67.6390 Cost 0.9609 RelCost 1.0382 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9014 0.9014 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.8809 0.8809 0.0 62 -4.0000 -4.0000 4.0000 -4.0000 4.0000 4.0000 0.8673 0.8673 0.0 68 -4.0000 -4.0000 4.0000 0.0000 0.0000 4.0000 0.8672 0.8672 0.0 191 -4.0000 4.0000 0.0000 -4.0000 -4.0000 4.0000 0.8630 0.8630 0.0 277 0.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8622 0.8622 0.0 309 0.0000 -4.0000 4.0000 0.0000 0.0000 -4.0000 0.8515 0.8515 0.0 Brute Force -------------------------- Min cost was 0.851544 Number of iterations 729 Search time 1.232000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 4.000 0.000 0.000 -4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 4 3 0 4 0 5 -4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.851544 2 1.000 -4.000 4.000 0.000 0.000 -4.000 0.8498202023 6 0.618 -4.000 4.000 0.000 0.000 -4.000 0.8486330903 8 0.774 -4.000 4.000 0.000 0.000 -4.000 0.8468892940 10 0.766 -4.000 4.000 0.000 0.000 -4.000 0.8468840482 11 0.765 -4.000 4.000 0.000 0.000 -4.000 0.8468827555 14 0.757 -4.000 4.000 0.000 0.000 -4.000 0.8468810863 15 0.760 -4.000 4.000 0.000 0.000 -4.000 0.8468801239 16 0.759 -4.000 4.000 0.000 0.000 -4.000 0.8468799878 23 0.759 -3.618 4.000 0.000 0.000 -4.000 0.8463561883 25 0.759 -3.796 4.000 0.000 0.000 -4.000 0.8461034517 26 0.759 -3.874 4.000 0.000 0.000 -4.000 0.8461021838 30 0.759 -3.860 4.000 0.000 0.000 -4.000 0.8460909914 32 0.759 -3.856 4.000 0.000 0.000 -4.000 0.8460907573 34 0.759 -3.854 4.000 0.000 0.000 -4.000 0.8460907270 36 0.759 -3.855 4.000 0.000 0.000 -4.000 0.8460906853 43 0.759 -3.855 3.869 0.000 0.000 -4.000 0.8449825274 58 0.759 -3.855 3.869 0.032 0.000 -4.000 0.8448763082 60 0.759 -3.855 3.869 0.038 0.000 -4.000 0.8448741297 61 0.759 -3.855 3.869 0.037 0.000 -4.000 0.8448739662 71 0.759 -3.855 3.869 0.037 0.027 -4.000 0.8445574879 72 0.759 -3.855 3.869 0.037 0.033 -4.000 0.8444984220 73 0.759 -3.855 3.869 0.037 0.049 -4.000 0.8443699397 76 0.759 -3.855 3.869 0.037 0.053 -4.000 0.8443483900 77 0.759 -3.855 3.869 0.037 0.055 -4.000 0.8443358302 78 0.759 -3.855 3.869 0.037 0.057 -4.000 0.8443284302 79 0.759 -3.855 3.869 0.037 0.058 -4.000 0.8443234971 84 0.759 -3.855 3.869 0.037 0.058 -4.618 0.8391297223 85 0.759 -3.855 3.869 0.037 0.058 -5.000 0.8360147433 87 0.759 -3.855 3.869 0.037 0.058 -4.965 0.8356637262 89 0.759 -3.855 3.869 0.037 0.058 -4.922 0.8345709780 92 0.759 -3.855 3.869 0.037 0.058 -4.920 0.8345616681 94 0.759 -3.855 3.869 0.037 0.058 -4.915 0.8345440828 95 0.759 -3.855 3.869 0.037 0.058 -4.912 0.8345332360 96 0.759 -3.855 3.869 0.037 0.058 -4.911 0.8345283620 powell nthiter 1: fret = 0.834528 114 0.756 -3.855 3.869 0.037 0.058 -4.911 0.8345068550 116 0.755 -3.855 3.869 0.037 0.058 -4.911 0.8344944045 124 0.755 -4.056 3.869 0.037 0.058 -4.911 0.8332190964 126 0.755 -3.987 3.869 0.037 0.058 -4.911 0.8321556220 139 0.755 -3.987 3.251 0.037 0.058 -4.911 0.8308026177 141 0.755 -3.987 3.492 0.037 0.058 -4.911 0.8292220498 144 0.755 -3.987 3.476 0.037 0.058 -4.911 0.8291880996 145 0.755 -3.987 3.477 0.037 0.058 -4.911 0.8291880448 153 0.755 -3.987 3.477 0.209 0.058 -4.911 0.8284893349 156 0.755 -3.987 3.477 0.239 0.058 -4.911 0.8283583796 157 0.755 -3.987 3.477 0.258 0.058 -4.911 0.8282904384 158 0.755 -3.987 3.477 0.270 0.058 -4.911 0.8282583273 161 0.755 -3.987 3.477 0.273 0.058 -4.911 0.8282563117 162 0.755 -3.987 3.477 0.274 0.058 -4.911 0.8282561865 163 0.755 -3.987 3.477 0.275 0.058 -4.911 0.8282557181 175 0.755 -3.987 3.477 0.275 0.064 -4.911 0.8282146905 188 0.755 -3.987 3.477 0.275 0.064 -4.874 0.8281611401 189 0.755 -3.987 3.477 0.275 0.064 -4.881 0.8281582619 192 0.755 -3.987 3.477 0.275 0.064 -4.886 0.8281567307 193 0.755 -3.987 3.477 0.275 0.064 -4.885 0.8281566218 powell nthiter 2: fret = 0.828157 202 0.678 -3.987 3.477 0.275 0.064 -4.885 0.8275275982 203 0.471 -3.987 3.477 0.275 0.064 -4.885 0.8271795059 204 0.538 -3.987 3.477 0.275 0.064 -4.885 0.8261160198 207 0.548 -3.987 3.477 0.275 0.064 -4.885 0.8260635186 210 0.551 -3.987 3.477 0.275 0.064 -4.885 0.8260461528 211 0.553 -3.987 3.477 0.275 0.064 -4.885 0.8260363935 221 0.553 -3.942 3.477 0.275 0.064 -4.885 0.8259991004 223 0.553 -3.925 3.477 0.275 0.064 -4.885 0.8259796936 224 0.553 -3.914 3.477 0.275 0.064 -4.885 0.8259746779 226 0.553 -3.918 3.477 0.275 0.064 -4.885 0.8259744700 227 0.553 -3.917 3.477 0.275 0.064 -4.885 0.8259741812 235 0.553 -3.917 3.593 0.275 0.064 -4.885 0.8241463484 236 0.553 -3.917 3.646 0.275 0.064 -4.885 0.8234294637 238 0.553 -3.917 3.649 0.275 0.064 -4.885 0.8234047449 241 0.553 -3.917 3.655 0.275 0.064 -4.885 0.8233664744 244 0.553 -3.917 3.656 0.275 0.064 -4.885 0.8233584436 277 0.553 -3.917 3.656 0.275 0.067 -4.885 0.8233349961 280 0.553 -3.917 3.656 0.275 0.068 -4.885 0.8233288301 powell nthiter 3: fret = 0.823329 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 0.878998 1 -25.0 -25.0 25.0 0.904334 2 -25.0 25.0 -25.0 0.917371 3 -25.0 25.0 25.0 0.889548 4 25.0 -25.0 -25.0 0.945359 5 25.0 -25.0 25.0 0.902385 6 25.0 25.0 -25.0 0.921602 7 25.0 25.0 25.0 0.926929 REL: 8 0.823329 7.286527 0.910816 rel = 0.903946 Number of iterations 3 Min cost was 0.823329 Number of FunctionCalls 385 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.684000 sec Parameters at optimum (transmm) 0.55284 -3.91663 3.65643 Parameters at optimum (rotdeg) 0.27482 0.06848 -4.88517 Final costs ---------------- Number of surface hits 2418 WM Intensity 0.0005 +/- 0.0002 Ctx Intensity 0.0005 +/- 0.0002 Pct Contrast -1579.0791 +/- 77298.1364 Cost 0.8233 RelCost 1.0382 Reg at min cost was 0.99637 0.08516 -0.00011 0.87885; -0.08516 0.99636 -0.00480 -3.69690; -0.00030 0.00480 0.99999 3.70096; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to ./tmp.bbregister.31499/bbr.pass1.dat, type = 14 Original Reg 1.00000 0.00000 -0.00089 0.30605; 0.00000 1.00000 0.00000 0.24690; 0.00089 0.00000 1.00000 0.04372; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00363 -0.08516 -0.00079 -0.57279; 0.08516 0.00364 0.00480 3.94381; 0.00120 -0.00480 0.00001 -3.65724; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 5.156662 Computing change in rh position Surface-RMS-Diff-mm 6.614064 1.853297 10.292881 mri_segreg done mri_segreg --mov ./tmp.bbregister.31499/template.nii --init-reg ./tmp.bbregister.31499/bbr.pass1.dat --out-reg output. dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost output.dat.mincost --dof 6 --nmax 36 - -param output.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.31499/reg.curopt.dat --gm-proj-fr ac 0.5 --nsub 1 --wm-gt-gm 0.5 $Id: mri_segreg.c,v 1.112 2014/02/25 19:06:37 greve Exp $ setenv SUBJECTS_DIR /analysis/nihapoe_roi_nnn/Converter/FS_DIR cd 04_baseline/mri mri_segreg --mov ./tmp.bbregister.31499/template.nii --init-reg ./tmp.bbregister.31499/bbr.pass1.dat --out-reg output. dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost output.dat.mincost --dof 6 --nmax 36 - -param output.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg ./tmp.bbregister.31499/reg.curopt.dat --gm-proj-fr ac 0.5 --nsub 1 --wm-gt-gm 0.5 sysname Linux hostname paialv03 machine x86_64 user pthiyyagura movvol ./tmp.bbregister.31499/template.nii regfile ./tmp.bbregister.31499/bbr.pass1.dat subject 10012004_baseline dof 6 outregfile output.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 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1456131708 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99637 0.08516 -0.00011 0.87885; -0.08516 0.99636 -0.00480 -3.69690; -0.00030 0.00480 0.99999 3.70096; 0.00000 0.00000 0.00000 1.00000; 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 for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.910477 1 -25.0 -25.0 25.0 0.890421 2 -25.0 25.0 -25.0 0.925189 3 -25.0 25.0 25.0 0.905317 4 25.0 -25.0 -25.0 0.939012 5 25.0 -25.0 25.0 0.931912 6 25.0 25.0 -25.0 0.921281 7 25.0 25.0 25.0 0.927262 REL: 8 0.875462 7.350870 0.918859 rel = 0.952772 Initial costs ---------------- Number of surface hits 241632 WM Intensity 0.0005 +/- 0.0002 Ctx Intensity 0.0005 +/- 0.0002 Pct Contrast -26.4898 +/- 8126.2438 Cost 0.8755 RelCost 0.9528 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8319 0.8319 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8279 0.8279 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8272 0.8272 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.8256 0.8256 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8223 0.8223 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.8216 0.8216 0.0 Brute Force -------------------------- Min cost was 0.821623 Number of iterations 729 Search time 1.159000 sec Parameters at best (transmm, rotdeg) -0.100 -0.100 0.000 0.000 0.000 0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -0.1 1 -0.1 2 0 3 0 4 0 5 0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.875940 2 0.900 -0.100 0.000 0.000 0.000 0.100 0.8711049979 3 2.518 -0.100 0.000 0.000 0.000 0.100 0.8702753920 4 1.864 -0.100 0.000 0.000 0.000 0.100 0.8684625017 11 1.901 -0.100 0.000 0.000 0.000 0.100 0.8684128274 15 1.900 -0.100 0.000 0.000 0.000 0.100 0.8684116212 16 1.899 -0.100 0.000 0.000 0.000 0.100 0.8684106791 18 1.899 0.900 0.000 0.000 0.000 0.100 0.8667968328 23 1.899 0.810 0.000 0.000 0.000 0.100 0.8667309994 28 1.899 0.809 0.000 0.000 0.000 0.100 0.8667295247 30 1.899 0.808 0.000 0.000 0.000 0.100 0.8667278641 36 1.899 0.808 0.382 0.000 0.000 0.100 0.8658565915 37 1.899 0.808 0.361 0.000 0.000 0.100 0.8658248523 39 1.899 0.808 0.358 0.000 0.000 0.100 0.8658169354 43 1.899 0.808 0.359 0.000 0.000 0.100 0.8658090677 59 1.899 0.808 0.359 -0.002 0.000 0.100 0.8658049817 60 1.899 0.808 0.359 -0.004 0.000 0.100 0.8658015741 66 1.899 0.808 0.359 -0.004 -0.618 0.100 0.8640761428 68 1.899 0.808 0.359 -0.004 -0.599 0.100 0.8640654852 69 1.899 0.808 0.359 -0.004 -0.530 0.100 0.8639360753 74 1.899 0.808 0.359 -0.004 -0.537 0.100 0.8639355823 75 1.899 0.808 0.359 -0.004 -0.534 0.100 0.8639294769 76 1.899 0.808 0.359 -0.004 -0.533 0.100 0.8639281729 77 1.899 0.808 0.359 -0.004 -0.532 0.100 0.8639279239 79 1.899 0.808 0.359 -0.004 -0.532 1.100 0.8627129252 83 1.899 0.808 0.359 -0.004 -0.532 0.718 0.8622877183 85 1.899 0.808 0.359 -0.004 -0.532 0.704 0.8622626393 powell nthiter 1: fret = 0.862263 97 2.281 0.808 0.359 -0.004 -0.532 0.704 0.8621754098 106 2.279 0.808 0.359 -0.004 -0.532 0.704 0.8621740905 107 2.278 0.808 0.359 -0.004 -0.532 0.704 0.8621733449 114 2.278 0.682 0.359 -0.004 -0.532 0.704 0.8621727889 115 2.278 0.744 0.359 -0.004 -0.532 0.704 0.8620568907 126 2.278 0.744 0.741 -0.004 -0.532 0.704 0.8614569185 127 2.278 0.744 0.647 -0.004 -0.532 0.704 0.8613490064 128 2.278 0.744 0.633 -0.004 -0.532 0.704 0.8613260093 130 2.278 0.744 0.593 -0.004 -0.532 0.704 0.8612671039 135 2.278 0.744 0.592 -0.004 -0.532 0.704 0.8612580810 161 2.278 0.744 0.592 -0.004 -0.477 0.704 0.8611961778 165 2.278 0.744 0.592 -0.004 -0.474 0.704 0.8611944917 168 2.278 0.744 0.592 -0.004 -0.473 0.704 0.8611941358 175 2.278 0.744 0.592 -0.004 -0.473 0.850 0.8611856081 176 2.278 0.744 0.592 -0.004 -0.473 0.794 0.8611649586 177 2.278 0.744 0.592 -0.004 -0.473 0.783 0.8611552494 180 2.278 0.744 0.592 -0.004 -0.473 0.787 0.8611515011 181 2.278 0.744 0.592 -0.004 -0.473 0.788 0.8611430825 powell nthiter 2: fret = 0.861143 191 1.982 0.744 0.592 -0.004 -0.473 0.788 0.8608037395 193 2.091 0.744 0.592 -0.004 -0.473 0.788 0.8607639208 195 2.044 0.744 0.592 -0.004 -0.473 0.788 0.8607531750 196 2.056 0.744 0.592 -0.004 -0.473 0.788 0.8607032355 198 2.055 0.744 0.592 -0.004 -0.473 0.788 0.8607029162 210 2.055 0.740 0.592 -0.004 -0.473 0.788 0.8606978074 224 2.055 0.740 0.596 -0.004 -0.473 0.788 0.8606953059 226 2.055 0.740 0.594 -0.004 -0.473 0.788 0.8606902302 227 2.055 0.740 0.593 -0.004 -0.473 0.788 0.8606900308 253 2.055 0.740 0.593 -0.004 -0.472 0.788 0.8606889355 269 2.055 0.740 0.593 -0.004 -0.472 0.789 0.8606859572 282 2.055 0.740 0.593 -0.004 -0.472 0.789 0.8606854833 284 2.054 0.740 0.593 -0.004 -0.472 0.789 0.8606846694 285 2.054 0.740 0.593 -0.004 -0.472 0.789 0.8606841788 powell nthiter 3: fret = 0.860684 297 2.054 0.740 0.593 -0.004 -0.472 0.799 0.8606818008 299 2.054 0.740 0.593 -0.004 -0.472 0.795 0.8606752431 301 2.054 0.740 0.593 -0.004 -0.472 0.796 0.8606734185 302 2.054 0.740 0.593 -0.004 -0.472 0.797 0.8606716642 351 2.054 0.740 0.593 -0.004 -0.478 0.797 0.8606634082 powell nthiter 4: fret = 0.860663 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.894803 1 -25.0 -25.0 25.0 0.894725 2 -25.0 25.0 -25.0 0.936964 3 -25.0 25.0 25.0 0.910313 4 25.0 -25.0 -25.0 0.924482 5 25.0 -25.0 25.0 0.933394 6 25.0 25.0 -25.0 0.917784 7 25.0 25.0 25.0 0.925553 REL: 8 0.860663 7.338019 0.917252 rel = 0.938306 Number of iterations 4 Min cost was 0.860663 Number of FunctionCalls 453 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 34.353000 sec Parameters at optimum (transmm) 2.05359 0.74032 0.59287 Parameters at optimum (rotdeg) -0.00382 -0.47819 0.79717 Final costs ---------------- Number of surface hits 241246 WM Intensity 0.0005 +/- 0.0002 Ctx Intensity 0.0005 +/- 0.0002 Pct Contrast -11.8632 +/- 1562.3176 Cost 0.8607 RelCost 0.9528 Reg at min cost was 0.99742 0.07125 -0.00839 2.95286; -0.07129 0.99744 -0.00486 -2.94418; 0.00802 0.00544 0.99995 4.30128; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to output.dat, type = 14 Original Reg 0.99637 0.08516 -0.00011 0.87885; -0.08516 0.99636 -0.00480 -3.69690; -0.00030 0.00480 0.99999 3.70096; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00106 0.01391 0.00828 -2.07402; -0.01387 -0.00109 0.00005 -0.75272; -0.00832 -0.00064 0.00004 -0.60032; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 2.176829 Computing change in rh position Surface-RMS-Diff-mm 2.383606 0.577578 3.664372 mri_segreg done MinCost: 0.860663 0.000513 0.000492 -11.863233 tkregister2_cmdl --mov ne/crsummed_LIA.nii --reg outpu t.dat --noedit --ltaout output.lta tkregister_tcl publicTool/free6surfer/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ne/crsummed_LIA.nii reg file output.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.99742 0.07125 -0.00839 2.95286; -0.07129 0.99744 -0.00486 -2.94418; 0.00802 0.00544 0.99995 4.30128; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target 04_baseline/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable ne/crsummed_LIA.nii Tmov: -------------------- -0.97656 0.00000 0.00000 93.75000; 0.00000 0.00000 1.50000 -108.00000; 0.00000 -0.97656 0.00000 125.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99742 0.07125 -0.00839 2.95286; -0.07129 0.99744 -0.00486 -2.94418; 0.00802 0.00544 0.99995 4.30128; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = 10012004_baseline RegMat --------------------------- 0.99742 0.07125 -0.00839 2.95286; -0.07129 0.99744 -0.00486 -2.94418; 0.00802 0.00544 0.99995 4.30128; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Fri Feb 12 11:31:49 MST 2016 Ended at Fri Feb 12 11:34:16 MST 2016 BBR-Run-Time-Sec 147 bbregister Done To check results, run: tkregister2 --mov ne/crsummed_LIA.nii --reg output.dat --surf