Logfile for bbregister s��b oct 15 23:08:01 CEST 2011 setenv SUBJECTS_DIR /home/joana/subjects cd /home/joana/Desktop/BEFREE/CN7 /usr/local/freesurfer5/freesurfer/bin/bbregister --s H_CN7 --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_CN7 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.19299/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.19299/fslregister --dof 6 Log file is ./tmp.bbregister.19299/reg.init.dat.fslregister.log s��b oct 15 23:08:02 CEST 2011 --s H_CN7 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.19299/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp ./tmp.bbregister.19299/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/CN7 mri_convert /home/joana/subjects/H_CN7/mri/brainmask.mgz ./tmp.bbregister.19299/fslregister/refvol.fslregister.nii mri_convert /home/joana/subjects/H_CN7/mri/brainmask.mgz ./tmp.bbregister.19299/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_CN7/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -4.19095e-09, -3.72529e-09) j_ras = (3.72529e-09, 5.96046e-08, -1) k_ras = (1.16415e-08, 1, -2.98023e-08) writing to ./tmp.bbregister.19299/fslregister/refvol.fslregister.nii... -------------------------------------- /home/joana/Desktop/BEFREE/CN7 mri_convert template_bbregister.nii.gz ./tmp.bbregister.19299/fslregister/movvol.fslregister.nii --frame 0 mri_convert template_bbregister.nii.gz ./tmp.bbregister.19299/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.19299/fslregister/movvol.fslregister.nii... Mov determinant is -10.9178 /home/joana/Desktop/BEFREE/CN7 tkregister2_cmdl --mov ./tmp.bbregister.19299/fslregister/movvol.fslregister.nii --reg ./tmp.bbregister.19299/fslregister/reg0.19346.dat --regheader --fslregout ./tmp.bbregister.19299/reg.init.dat.fsl.mat0 --s H_CN7 --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.19299/fslregister/movvol.fslregister.nii reg file ./tmp.bbregister.19299/fslregister/reg0.19346.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_CN7/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.19299/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 -125.859; 0.000 -0.000 1.000 -43.059; -0.000 -1.000 0.000 131.213; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 0.000 -0.000 -125.859; 0.000 -0.000 1.000 -43.059; -0.000 -1.000 0.000 131.213; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN7 RegMat --------------------------- 1.000 0.000 -0.000 -125.859; 0.000 -0.000 1.000 -43.059; -0.000 -1.000 0.000 131.213; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -10.9178, ref det = -1 s��b oct 15 23:08:06 CEST 2011 /home/joana/Desktop/BEFREE/CN7 flirt.fsl -ref ./tmp.bbregister.19299/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.19299/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.19299/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl-4.1.6//etc/flirtsch/xyztrans.sch -init ./tmp.bbregister.19299/reg.init.dat.fsl.mat0 s��b oct 15 23:08:15 CEST 2011 /home/joana/Desktop/BEFREE/CN7 flirt.fsl -ref ./tmp.bbregister.19299/fslregister/refvol.fslregister.nii -in ./tmp.bbregister.19299/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat ./tmp.bbregister.19299/reg.init.dat.fsl.mat -init ./tmp.bbregister.19299/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer5/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s H_CN7 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.19299/reg.init.dat --fslreg ./tmp.bbregister.19299/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer5/freesurfer/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.986 -0.003 0.165 -3.013; 0.153 0.390 -0.908 104.483; -0.061 0.921 0.385 2.734; 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.19299/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_CN7/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) -------- 0.986 0.061 0.153 -0.117; -0.165 0.385 0.908 -8.776; -0.003 -0.921 0.390 0.863; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.986 0.061 0.153 -0.117; -0.165 0.385 0.908 -8.776; -0.003 -0.921 0.390 0.863; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN7 RegMat --------------------------- 0.986 0.061 0.153 -0.117; -0.165 0.385 0.908 -8.776; -0.003 -0.921 0.390 0.863; 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 s��b oct 15 23:08:02 CEST 2011 Ended at s��b oct 15 23:08:29 CEST 2011 fslregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg ./tmp.bbregister.19299/reg.init.dat --surf orig mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.19299/reg.init.dat --out-reg ./tmp.bbregister.19299/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/CN7 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.19299/reg.init.dat --out-reg ./tmp.bbregister.19299/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.19299/reg.init.dat subject H_CN7 dof 6 outregfile ./tmp.bbregister.19299/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 1319276798 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.986 0.061 0.153 -0.117; -0.165 0.385 0.908 -8.776; -0.003 -0.921 0.390 0.863; 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 1.042750 1 -25.0 -25.0 25.0 0.981585 2 -25.0 25.0 -25.0 1.000852 3 -25.0 25.0 25.0 1.057366 4 25.0 -25.0 -25.0 1.019158 5 25.0 -25.0 25.0 1.004667 6 25.0 25.0 -25.0 1.014722 7 25.0 25.0 25.0 1.048107 REL: 8 0.927615 8.169207 1.021151 rel = 0.908402 Initial costs ---------------- Number of surface hits 2404 WM Intensity 544.3542 +/- 193.3530 Ctx Intensity 560.3570 +/- 210.0541 Pct Contrast 2.1217 +/- 33.0536 Cost 0.9276 RelCost 0.9084 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0138 1.0138 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9562 0.9562 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9466 0.9466 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9163 0.9163 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9134 0.9134 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8977 0.8977 0.0 8 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 4.0000 0.8917 0.8917 0.0 29 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 4.0000 0.8890 0.8890 0.0 Brute Force -------------------------- Min cost was 0.888952 Number of iterations 729 Search time 2.140000 sec Parameters at best (transmm, rotdeg) -4.000 -4.000 0.000 -4.000 -4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 -4 1 -4 2 0 3 -4 4 -4 5 4 6 -3.618 -4.000 0.000 -4.000 -4.000 4.000 0.8859129709 8 -3.762 -4.000 0.000 -4.000 -4.000 4.000 0.8824279967 10 -3.765 -4.000 0.000 -4.000 -4.000 4.000 0.8823967970 11 -3.784 -4.000 0.000 -4.000 -4.000 4.000 0.8822922043 19 -3.784 -3.618 0.000 -4.000 -4.000 4.000 0.8812443522 21 -3.784 -3.595 0.000 -4.000 -4.000 4.000 0.8805877278 26 -3.784 -3.603 0.000 -4.000 -4.000 4.000 0.8805463380 31 -3.784 -3.604 0.000 -4.000 -4.000 4.000 0.8805422685 38 -3.784 -3.604 -0.150 -4.000 -4.000 4.000 0.8795523263 43 -3.784 -3.604 -0.154 -4.000 -4.000 4.000 0.8795403988 44 -3.784 -3.604 -0.156 -4.000 -4.000 4.000 0.8795332223 52 -3.784 -3.604 -0.156 -3.618 -4.000 4.000 0.8756873142 54 -3.784 -3.604 -0.156 -3.774 -4.000 4.000 0.8751765838 56 -3.784 -3.604 -0.156 -3.710 -4.000 4.000 0.8745264299 57 -3.784 -3.604 -0.156 -3.707 -4.000 4.000 0.8745229130 58 -3.784 -3.604 -0.156 -3.705 -4.000 4.000 0.8745210385 61 -3.784 -3.604 -0.156 -3.703 -4.000 4.000 0.8745209140 62 -3.784 -3.604 -0.156 -3.702 -4.000 4.000 0.8745208728 71 -3.784 -3.604 -0.156 -3.702 -4.052 4.000 0.8740817584 72 -3.784 -3.604 -0.156 -3.702 -4.048 4.000 0.8740172133 73 -3.784 -3.604 -0.156 -3.702 -4.035 4.000 0.8739621429 75 -3.784 -3.604 -0.156 -3.702 -4.038 4.000 0.8739519007 84 -3.784 -3.604 -0.156 -3.702 -4.038 3.980 0.8736335850 87 -3.784 -3.604 -0.156 -3.702 -4.038 3.970 0.8735702475 90 -3.784 -3.604 -0.156 -3.702 -4.038 3.968 0.8735633775 91 -3.784 -3.604 -0.156 -3.702 -4.038 3.967 0.8735621962 92 -3.784 -3.604 -0.156 -3.702 -4.038 3.966 0.8735618616 116 -3.784 -3.510 -0.156 -3.702 -4.038 3.966 0.8722487985 119 -3.784 -3.509 -0.156 -3.702 -4.038 3.966 0.8722483540 127 -3.784 -3.509 -0.179 -3.702 -4.038 3.966 0.8720868756 128 -3.784 -3.509 -0.249 -3.702 -4.038 3.966 0.8718019873 131 -3.784 -3.509 -0.226 -3.702 -4.038 3.966 0.8717368561 133 -3.784 -3.509 -0.225 -3.702 -4.038 3.966 0.8717367955 143 -3.784 -3.509 -0.224 -3.644 -4.038 3.966 0.8716544264 150 -3.784 -3.509 -0.224 -3.647 -4.038 3.966 0.8715703484 151 -3.784 -3.509 -0.224 -3.650 -4.038 3.966 0.8715373719 166 -3.784 -3.509 -0.224 -3.650 -4.033 3.966 0.8714873931 167 -3.784 -3.509 -0.224 -3.650 -4.029 3.966 0.8714628101 179 -3.784 -3.509 -0.224 -3.650 -4.029 4.014 0.8711243794 180 -3.784 -3.509 -0.224 -3.650 -4.029 4.010 0.8711238086 181 -3.784 -3.509 -0.224 -3.650 -4.029 4.012 0.8711225414 191 -3.795 -3.509 -0.224 -3.650 -4.029 4.012 0.8708738997 192 -3.813 -3.509 -0.224 -3.650 -4.029 4.012 0.8705868757 194 -3.819 -3.509 -0.224 -3.650 -4.029 4.012 0.8705707332 196 -3.820 -3.509 -0.224 -3.650 -4.029 4.012 0.8705707248 209 -3.820 -3.510 -0.224 -3.650 -4.029 4.012 0.8705705505 218 -3.820 -3.510 -0.229 -3.650 -4.029 4.012 0.8705568469 219 -3.820 -3.510 -0.230 -3.650 -4.029 4.012 0.8705555146 220 -3.820 -3.510 -0.232 -3.650 -4.029 4.012 0.8705541556 229 -3.820 -3.510 -0.232 -3.655 -4.029 4.012 0.8705009514 230 -3.820 -3.510 -0.232 -3.673 -4.029 4.012 0.8704426526 233 -3.820 -3.510 -0.232 -3.680 -4.029 4.012 0.8704126648 234 -3.820 -3.510 -0.232 -3.684 -4.029 4.012 0.8703957622 235 -3.820 -3.510 -0.232 -3.687 -4.029 4.012 0.8703863261 245 -3.820 -3.510 -0.232 -3.687 -3.971 4.012 0.8703514761 246 -3.820 -3.510 -0.232 -3.687 -3.999 4.012 0.8701306740 248 -3.820 -3.510 -0.232 -3.687 -3.993 4.012 0.8701046363 250 -3.820 -3.510 -0.232 -3.687 -3.991 4.012 0.8701009211 251 -3.820 -3.510 -0.232 -3.687 -3.990 4.012 0.8701007789 260 -3.820 -3.510 -0.232 -3.687 -3.990 4.045 0.8700180122 262 -3.820 -3.510 -0.232 -3.687 -3.990 4.030 0.8697600154 263 -3.820 -3.510 -0.232 -3.687 -3.990 4.023 0.8696818397 264 -3.820 -3.510 -0.232 -3.687 -3.990 4.019 0.8696482771 265 -3.820 -3.510 -0.232 -3.687 -3.990 4.016 0.8696355075 266 -3.820 -3.510 -0.232 -3.687 -3.990 4.014 0.8696301862 267 -3.820 -3.510 -0.232 -3.687 -3.990 4.013 0.8696283764 277 -3.837 -3.510 -0.232 -3.687 -3.990 4.013 0.8693905968 278 -3.845 -3.510 -0.232 -3.687 -3.990 4.013 0.8693717003 279 -3.844 -3.510 -0.232 -3.687 -3.990 4.013 0.8693688143 280 -3.843 -3.510 -0.232 -3.687 -3.990 4.013 0.8693664784 304 -3.843 -3.510 -0.210 -3.687 -3.990 4.013 0.8693025247 305 -3.843 -3.510 -0.217 -3.687 -3.990 4.013 0.8692888352 306 -3.843 -3.510 -0.216 -3.687 -3.990 4.013 0.8692885109 330 -3.843 -3.510 -0.216 -3.687 -3.985 4.013 0.8692807243 331 -3.843 -3.510 -0.216 -3.687 -3.987 4.013 0.8692772028 357 -3.844 -3.510 -0.216 -3.687 -3.987 4.013 0.8692771017 392 -3.844 -3.510 -0.216 -3.685 -3.987 4.013 0.8692769781 404 -3.844 -3.510 -0.216 -3.685 -3.986 4.013 0.8692758171 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.000124 1 -25.0 -25.0 25.0 1.014570 2 -25.0 25.0 -25.0 1.042461 3 -25.0 25.0 25.0 1.052380 4 25.0 -25.0 -25.0 1.009437 5 25.0 -25.0 25.0 1.033121 6 25.0 25.0 -25.0 1.029073 7 25.0 25.0 25.0 1.041300 REL: 8 0.869276 8.222466 1.027808 rel = 0.845757 Number of iterations 4 Min cost was 0.869276 Number of FunctionCalls 418 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 1.225000 sec Parameters at optimum (transmm) -3.84376 -3.50971 -0.21593 Parameters at optimum (rotdeg) -3.68543 -3.98581 4.01322 Final costs ---------------- Number of surface hits 2385 WM Intensity 531.8184 +/- 191.0414 Ctx Intensity 546.8727 +/- 204.0628 Pct Contrast 1.7437 +/- 35.4200 Cost 0.8693 RelCost 0.9084 Reg at min cost was 0.993 0.104 0.064 -3.450; -0.095 0.333 0.938 -12.205; 0.076 -0.937 0.340 1.198; 0.000 0.000 0.000 1.000; Writing optimal reg to ./tmp.bbregister.19299/bbr.pass1.dat, type = 14 Original Reg 0.986 0.061 0.153 -0.117; -0.165 0.385 0.908 -8.776; -0.003 -0.921 0.390 0.863; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.006 -0.042 0.089 3.333; -0.069 0.052 -0.030 3.430; -0.079 0.016 0.049 -0.335; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 7.417756 Computing change in rh position Surface RMS Diff (mm) 6.835730 10.670351 mri_segreg done mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.19299/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.19299/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/CN7 mri_segreg --mov template_bbregister.nii.gz --init-reg ./tmp.bbregister.19299/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.19299/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.19299/bbr.pass1.dat subject H_CN7 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 1319678508 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.993 0.104 0.064 -3.450; -0.095 0.333 0.938 -12.205; 0.076 -0.937 0.340 1.198; 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 0.995081 1 -25.0 -25.0 25.0 1.032958 2 -25.0 25.0 -25.0 1.029672 3 -25.0 25.0 25.0 1.021198 4 25.0 -25.0 -25.0 1.012841 5 25.0 -25.0 25.0 1.013959 6 25.0 25.0 -25.0 1.017937 7 25.0 25.0 25.0 1.037575 REL: 8 0.957495 8.161221 1.020153 rel = 0.93858 Initial costs ---------------- Number of surface hits 239934 WM Intensity 532.9111 +/- 189.2585 Ctx Intensity 539.4360 +/- 202.6576 Pct Contrast -0.3512 +/- 35.5683 Cost 0.9575 RelCost 0.9386 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 0.8837 0.8837 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8826 0.8826 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8801 0.8801 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8788 0.8788 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8768 0.8768 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.8761 0.8761 0.0 23 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.8753 0.8753 0.0 50 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.8750 0.8750 0.0 70 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.0000 0.8746 0.8746 0.0 71 -0.1000 -0.1000 0.1000 0.0000 0.1000 0.1000 0.8745 0.8745 0.0 104 -0.1000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.8735 0.8735 0.0 105 -0.1000 0.0000 -0.1000 0.1000 0.1000 -0.1000 0.8735 0.8735 0.0 106 -0.1000 0.0000 -0.1000 0.1000 0.1000 0.0000 0.8733 0.8733 0.0 131 -0.1000 0.0000 0.0000 0.1000 0.0000 0.1000 0.8721 0.8721 0.0 265 0.0000 -0.1000 -0.1000 0.1000 0.0000 0.0000 0.8720 0.8720 0.0 344 0.0000 0.0000 -0.1000 0.1000 -0.1000 0.1000 0.8717 0.8717 0.0 346 0.0000 0.0000 -0.1000 0.1000 0.0000 0.0000 0.8710 0.8710 0.0 347 0.0000 0.0000 -0.1000 0.1000 0.0000 0.1000 0.8706 0.8706 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.8693 0.8693 0.0 Brute Force -------------------------- Min cost was 0.869276 Number of iterations 729 Search time 2.082000 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 3 -1.618 0.000 0.000 0.000 0.000 0.000 0.9550719457 4 -2.154 0.000 0.000 0.000 0.000 0.000 0.9538923133 5 -3.020 0.000 0.000 0.000 0.000 0.000 0.9534988979 11 -3.127 0.000 0.000 0.000 0.000 0.000 0.9533181158 12 -3.265 0.000 0.000 0.000 0.000 0.000 0.9531099399 14 -3.256 0.000 0.000 0.000 0.000 0.000 0.9530998503 16 -3.245 0.000 0.000 0.000 0.000 0.000 0.9530983846 17 -3.249 0.000 0.000 0.000 0.000 0.000 0.9530941027 22 -3.249 -1.618 0.000 0.000 0.000 0.000 0.9444363879 23 -3.249 -2.300 0.000 0.000 0.000 0.000 0.9442352977 43 -3.249 -1.622 0.382 0.000 0.000 0.000 0.9441162266 45 -3.249 -1.622 0.618 0.000 0.000 0.000 0.9440286442 46 -3.249 -1.622 0.579 0.000 0.000 0.000 0.9439826700 48 -3.249 -1.622 0.577 0.000 0.000 0.000 0.9439764196 49 -3.249 -1.622 0.556 0.000 0.000 0.000 0.9439454759 50 -3.249 -1.622 0.557 0.000 0.000 0.000 0.9439452721 53 -3.249 -1.622 0.557 1.000 0.000 0.000 0.9426667559 58 -3.249 -1.622 0.557 0.834 0.000 0.000 0.9426417335 59 -3.249 -1.622 0.557 0.872 0.000 0.000 0.9425929904 60 -3.249 -1.622 0.557 0.910 0.000 0.000 0.9425444541 62 -3.249 -1.622 0.557 0.909 0.000 0.000 0.9425398750 69 -3.249 -1.622 0.557 0.909 -1.618 0.000 0.9406123474 70 -3.249 -1.622 0.557 0.909 -1.145 0.000 0.9402118966 72 -3.249 -1.622 0.557 0.909 -0.707 0.000 0.9397828252 74 -3.249 -1.622 0.557 0.909 -0.754 0.000 0.9397792207 75 -3.249 -1.622 0.557 0.909 -0.743 0.000 0.9397667888 76 -3.249 -1.622 0.557 0.909 -0.732 0.000 0.9397445397 80 -3.249 -1.622 0.557 0.909 -0.731 0.000 0.9397445130 86 -3.249 -1.622 0.557 0.909 -0.731 -0.618 0.9397017181 88 -3.249 -1.622 0.557 0.909 -0.731 -0.347 0.9395649806 90 -3.249 -1.622 0.557 0.909 -0.731 -0.452 0.9395376828 93 -3.249 -1.622 0.557 0.909 -0.731 -0.441 0.9395216419 95 -3.249 -1.622 0.557 0.909 -0.731 -0.442 0.9395181726 96 -3.249 -1.622 0.557 0.909 -0.731 -0.446 0.9395068624 109 -3.230 -1.622 0.557 0.909 -0.731 -0.446 0.9394748549 110 -3.199 -1.622 0.557 0.909 -0.731 -0.446 0.9394698461 111 -3.163 -1.622 0.557 0.909 -0.731 -0.446 0.9394322575 116 -3.159 -1.622 0.557 0.909 -0.731 -0.446 0.9394247384 129 -3.159 -1.631 0.557 0.909 -0.731 -0.446 0.9394144835 137 -3.159 -1.631 -0.061 0.909 -0.731 -0.446 0.9394066174 139 -3.159 -1.631 0.243 0.909 -0.731 -0.446 0.9391744352 140 -3.159 -1.631 0.246 0.909 -0.731 -0.446 0.9391631432 141 -3.159 -1.631 0.365 0.909 -0.731 -0.446 0.9389786532 142 -3.159 -1.631 0.349 0.909 -0.731 -0.446 0.9389689527 152 -3.159 -1.631 0.349 1.291 -0.731 -0.446 0.9386108175 153 -3.159 -1.631 0.349 1.402 -0.731 -0.446 0.9385476992 157 -3.159 -1.631 0.349 1.430 -0.731 -0.446 0.9385380435 159 -3.159 -1.631 0.349 1.420 -0.731 -0.446 0.9385037172 160 -3.159 -1.631 0.349 1.413 -0.731 -0.446 0.9384947061 171 -3.159 -1.631 0.349 1.413 -0.831 -0.446 0.9383280960 173 -3.159 -1.631 0.349 1.413 -0.858 -0.446 0.9382654905 175 -3.159 -1.631 0.349 1.413 -0.865 -0.446 0.9382603449 177 -3.159 -1.631 0.349 1.413 -0.863 -0.446 0.9382581721 183 -3.159 -1.631 0.349 1.413 -0.863 -1.064 0.9379144671 186 -3.159 -1.631 0.349 1.413 -0.863 -1.210 0.9378278277 188 -3.159 -1.631 0.349 1.413 -0.863 -1.154 0.9377453866 191 -3.159 -1.631 0.349 1.413 -0.863 -1.161 0.9377384250 192 -3.159 -1.631 0.349 1.413 -0.863 -1.162 0.9377315187 193 -3.159 -1.631 0.349 1.413 -0.863 -1.166 0.9377292986 196 -3.159 -1.631 0.349 1.413 -0.863 -1.167 0.9377276522 205 -3.091 -1.631 0.349 1.413 -0.863 -1.167 0.9377070431 206 -3.120 -1.631 0.349 1.413 -0.863 -1.167 0.9376347009 209 -3.118 -1.631 0.349 1.413 -0.863 -1.167 0.9376293269 219 -3.118 -1.588 0.349 1.413 -0.863 -1.167 0.9375721444 223 -3.118 -1.591 0.349 1.413 -0.863 -1.167 0.9375681364 231 -3.118 -1.591 -0.269 1.413 -0.863 -1.167 0.9370200037 232 -3.118 -1.591 -0.651 1.413 -0.863 -1.167 0.9369583105 233 -3.118 -1.591 -0.572 1.413 -0.863 -1.167 0.9367821855 234 -3.118 -1.591 -0.471 1.413 -0.863 -1.167 0.9367454275 235 -3.118 -1.591 -0.503 1.413 -0.863 -1.167 0.9366882998 236 -3.118 -1.591 -0.515 1.413 -0.863 -1.167 0.9366820052 238 -3.118 -1.591 -0.511 1.413 -0.863 -1.167 0.9366722460 265 -3.118 -1.591 -0.511 1.413 -0.481 -1.167 0.9362289587 268 -3.118 -1.591 -0.511 1.413 -0.396 -1.167 0.9360350853 271 -3.118 -1.591 -0.511 1.413 -0.404 -1.167 0.9360257552 278 -3.118 -1.591 -0.511 1.413 -0.404 -1.785 0.9355924006 279 -3.118 -1.591 -0.511 1.413 -0.404 -2.167 0.9355421675 285 -3.118 -1.591 -0.511 1.413 -0.404 -2.172 0.9355332948 287 -3.118 -1.591 -0.511 1.413 -0.404 -2.173 0.9355300231 288 -3.118 -1.591 -0.511 1.413 -0.404 -2.175 0.9355295681 302 -3.084 -1.591 -0.511 1.413 -0.404 -2.175 0.9355083898 303 -3.093 -1.591 -0.511 1.413 -0.404 -2.175 0.9354858330 305 -3.094 -1.591 -0.511 1.413 -0.404 -2.175 0.9354841089 311 -3.094 -2.209 -0.511 1.413 -0.404 -2.175 0.9348810774 312 -3.094 -2.591 -0.511 1.413 -0.404 -2.175 0.9340359333 317 -3.094 -2.590 -0.511 1.413 -0.404 -2.175 0.9340314485 319 -3.094 -2.584 -0.511 1.413 -0.404 -2.175 0.9340180385 320 -3.094 -2.583 -0.511 1.413 -0.404 -2.175 0.9340147390 327 -3.094 -2.583 -1.129 1.413 -0.404 -2.175 0.9335966157 329 -3.094 -2.583 -0.942 1.413 -0.404 -2.175 0.9334483737 330 -3.094 -2.583 -0.920 1.413 -0.404 -2.175 0.9334251844 331 -3.094 -2.583 -0.764 1.413 -0.404 -2.175 0.9332648195 333 -3.094 -2.583 -0.792 1.413 -0.404 -2.175 0.9332253217 334 -3.094 -2.583 -0.841 1.413 -0.404 -2.175 0.9331852270 338 -3.094 -2.583 -0.834 1.413 -0.404 -2.175 0.9331753354 339 -3.094 -2.583 -0.833 1.413 -0.404 -2.175 0.9331747264 342 -3.094 -2.583 -0.833 2.413 -0.404 -2.175 0.9323357902 345 -3.094 -2.583 -0.833 3.031 -0.404 -2.175 0.9319887535 347 -3.094 -2.583 -0.833 2.797 -0.404 -2.175 0.9314894657 349 -3.094 -2.583 -0.833 2.841 -0.404 -2.175 0.9314225877 363 -3.094 -2.583 -0.833 2.841 -0.286 -2.175 0.9313369022 364 -3.094 -2.583 -0.833 2.841 -0.306 -2.175 0.9313212307 368 -3.094 -2.583 -0.833 2.841 -0.308 -2.175 0.9313193991 370 -3.094 -2.583 -0.833 2.841 -0.307 -2.175 0.9313165385 375 -3.094 -2.583 -0.833 2.841 -0.307 -2.793 0.9313129323 377 -3.094 -2.583 -0.833 2.841 -0.307 -2.485 0.9304667803 394 -3.090 -2.583 -0.833 2.841 -0.307 -2.485 0.9304642310 395 -3.087 -2.583 -0.833 2.841 -0.307 -2.485 0.9304606674 404 -3.087 -2.518 -0.833 2.841 -0.307 -2.485 0.9304378703 405 -3.087 -2.535 -0.833 2.841 -0.307 -2.485 0.9304303422 419 -3.087 -2.535 -0.765 2.841 -0.307 -2.485 0.9303434750 420 -3.087 -2.535 -0.762 2.841 -0.307 -2.485 0.9303342710 421 -3.087 -2.535 -0.733 2.841 -0.307 -2.485 0.9303124978 422 -3.087 -2.535 -0.740 2.841 -0.307 -2.485 0.9303058442 424 -3.087 -2.535 -0.738 2.841 -0.307 -2.485 0.9303032848 425 -3.087 -2.535 -0.739 2.841 -0.307 -2.485 0.9303025816 446 -3.087 -2.535 -0.739 2.841 -0.184 -2.485 0.9299160416 447 -3.087 -2.535 -0.739 2.841 -0.160 -2.485 0.9299148380 479 -3.089 -2.535 -0.739 2.841 -0.160 -2.485 0.9299080131 493 -3.089 -2.536 -0.739 2.841 -0.160 -2.485 0.9299038099 494 -3.089 -2.537 -0.739 2.841 -0.160 -2.485 0.9298981756 502 -3.089 -2.537 -0.763 2.841 -0.160 -2.485 0.9297962221 503 -3.089 -2.537 -0.838 2.841 -0.160 -2.485 0.9297055443 505 -3.089 -2.537 -0.825 2.841 -0.160 -2.485 0.9297002471 506 -3.089 -2.537 -0.823 2.841 -0.160 -2.485 0.9296922552 511 -3.089 -2.537 -0.824 2.841 -0.160 -2.485 0.9296918311 520 -3.089 -2.537 -0.824 2.873 -0.160 -2.485 0.9296446055 522 -3.089 -2.537 -0.824 2.874 -0.160 -2.485 0.9296389625 526 -3.089 -2.537 -0.824 2.875 -0.160 -2.485 0.9296384072 533 -3.089 -2.537 -0.824 2.875 -0.133 -2.485 0.9296293714 538 -3.089 -2.537 -0.824 2.875 -0.125 -2.485 0.9296242493 540 -3.089 -2.537 -0.824 2.875 -0.124 -2.485 0.9296227829 542 -3.089 -2.537 -0.824 2.875 -0.123 -2.485 0.9296209732 558 -3.089 -2.537 -0.824 2.875 -0.123 -2.487 0.9296192208 571 -3.086 -2.537 -0.824 2.875 -0.123 -2.487 0.9296190236 574 -3.085 -2.537 -0.824 2.875 -0.123 -2.487 0.9296136760 585 -3.085 -2.517 -0.824 2.875 -0.123 -2.487 0.9295991715 600 -3.085 -2.517 -0.848 2.875 -0.123 -2.487 0.9295905174 601 -3.085 -2.517 -0.845 2.875 -0.123 -2.487 0.9295846834 602 -3.085 -2.517 -0.838 2.875 -0.123 -2.487 0.9295739528 603 -3.085 -2.517 -0.832 2.875 -0.123 -2.487 0.9295634839 605 -3.085 -2.517 -0.833 2.875 -0.123 -2.487 0.9295620127 643 -3.085 -2.517 -0.833 2.875 -0.123 -2.486 0.9295551426 656 -3.086 -2.517 -0.833 2.875 -0.123 -2.486 0.9295529068 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 0.987149 1 -25.0 -25.0 25.0 1.013032 2 -25.0 25.0 -25.0 1.046758 3 -25.0 25.0 25.0 1.006656 4 25.0 -25.0 -25.0 1.040459 5 25.0 -25.0 25.0 1.007591 6 25.0 25.0 -25.0 0.997428 7 25.0 25.0 25.0 1.017474 REL: 8 0.929553 8.116549 1.014569 rel = 0.916205 Number of iterations 8 Min cost was 0.929553 Number of FunctionCalls 808 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 120.275000 sec Parameters at optimum (transmm) -3.08553 -2.51708 -0.83345 Parameters at optimum (rotdeg) 2.87542 -0.12300 -2.48608 Final costs ---------------- Number of surface hits 225673 WM Intensity 527.5310 +/- 198.6478 Ctx Intensity 537.5731 +/- 213.2466 Pct Contrast 0.3445 +/- 36.9641 Cost 0.9296 RelCost 0.9386 Reg at min cost was 0.987 0.122 0.103 -7.065; -0.142 0.375 0.916 -14.606; 0.073 -0.919 0.387 -0.257; 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 0.993 0.104 0.064 -3.450; -0.095 0.333 0.938 -12.205; 0.076 -0.937 0.340 1.198; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.005 -0.018 -0.039 3.615; 0.047 -0.042 0.022 2.401; 0.003 -0.018 -0.047 1.455; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 5.000754 Computing change in rh position Surface RMS Diff (mm) 5.740343 10.134857 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 -------- 0.987 0.122 0.103 -7.065; -0.142 0.375 0.916 -14.606; 0.073 -0.919 0.387 -0.257; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/joana/subjects/H_CN7/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 -------- 0.987 0.122 0.103 -7.065; -0.142 0.375 0.916 -14.606; 0.073 -0.919 0.387 -0.257; 0.000 0.000 0.000 1.000; Determinant 1 subject = H_CN7 RegMat --------------------------- 0.987 0.122 0.103 -7.065; -0.142 0.375 0.916 -14.606; 0.073 -0.919 0.387 -0.257; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -10.9178, ref det = -1 Cleaning up Started at s��b oct 15 23:08:01 CEST 2011 Ended at s��b oct 15 23:11:03 CEST 2011 BBR-Run-Time-Sec 182 bbregister Done To check results, run: tkregister2 --mov template_bbregister.nii.gz --reg register.dat --surf