Logfile for bbregister Thu Aug 8 23:20:09 CEST 2013 setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts /opt/freesurfer/5.3.0/bin/bbregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --lta /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta --init-fsl --T2 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer/5.3.0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii... fslregister --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz Log file is /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fslregister.log Thu Aug 8 23:20:14 CEST 2013 --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ snake5 Linux snake5 2.6.32-5-amd64 #1 SMP Fri May 10 08:43:19 UTC 2013 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-09, 1.86265e-09) j_ras = (-1.86265e-09, 1.49012e-08, -1) k_ras = (9.31323e-10, 1, -1.49012e-08) writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii... -------------------------------------- /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0 mri_convert /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998757, 0.0408089, 0.02861) j_ras = (0.0441177, 0.99097, 0.126615) k_ras = (0.0231846, -0.12772, 0.991539) keeping frame 0 writing to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii... Mov determinant is -0.311076 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.dat --regheader --fslregout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 --s sub006 --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/reg0.19186.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/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii Tmov: -------------------- -0.700 0.000 0.000 95.889; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.041 -0.029 -0.000; 0.023 -0.128 0.992 -0.000; -0.044 -0.991 -0.127 0.000; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -0.311076, ref det = -1 Thu Aug 8 23:20:22 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/xyztrans.sch -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat0 Thu Aug 8 23:24:44 CEST 2013 /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts flirt.fsl -ref /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/refvol.fslregister.nii -in /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat -init /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/fslregister/fslmat0.trans.mat -schedule /opt/freesurfer/5.3.0/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub006 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --fslreg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat.fsl.mat --noedit tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 -0.042 -0.020 40.136; -0.025 -0.120 -0.992 274.192; 0.039 0.992 -0.121 12.050; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii Tmov: -------------------- -0.700 0.000 0.000 95.889; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -0.311076, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Started at Thu Aug 8 23:20:14 CEST 2013 Ended at Thu Aug 8 23:31:25 CEST 2013 fslregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --surf orig mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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 snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.init.dat subject sub006 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/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 1376052073 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 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 0.990036 1 -25.0 -25.0 25.0 1.013869 2 -25.0 25.0 -25.0 1.045360 3 -25.0 25.0 25.0 1.003149 4 25.0 -25.0 -25.0 1.023281 5 25.0 -25.0 25.0 1.006686 6 25.0 25.0 -25.0 1.010024 7 25.0 25.0 25.0 1.048604 REL: 8 0.322576 8.141011 1.017626 rel = 0.316989 Initial costs ---------------- Number of surface hits 3238 WM Intensity 61.7561 +/- 11.7398 Ctx Intensity 77.7046 +/- 15.1309 Pct Contrast 22.3549 +/- 23.0208 Cost 0.3226 RelCost 0.3170 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9854 0.9854 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9791 0.9791 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9606 0.9606 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9556 0.9556 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8671 0.8671 0.0 21 -4.0000 -4.0000 -4.0000 4.0000 0.0000 -4.0000 0.8189 0.8189 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7643 0.7643 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6566 0.6566 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6078 0.6078 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3226 0.3226 0.0 Brute Force -------------------------- Min cost was 0.322576 Number of iterations 729 Search time 2.528000 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 10 -0.006 0.000 0.000 0.000 0.000 0.000 0.3225513539 11 -0.005 0.000 0.000 0.000 0.000 0.000 0.3225499366 15 -0.005 -1.618 0.000 0.000 0.000 0.000 0.1223710691 20 -0.005 -1.431 0.000 0.000 0.000 0.000 0.1196453081 21 -0.005 -1.460 0.000 0.000 0.000 0.000 0.1190840389 22 -0.005 -1.491 0.000 0.000 0.000 0.000 0.1184857389 24 -0.005 -1.500 0.000 0.000 0.000 0.000 0.1184697786 25 -0.005 -1.498 0.000 0.000 0.000 0.000 0.1184583008 26 -0.005 -1.496 0.000 0.000 0.000 0.000 0.1184563610 29 -0.005 -1.496 1.000 0.000 0.000 0.000 0.1170204377 33 -0.005 -1.496 0.618 0.000 0.000 0.000 0.0877717013 35 -0.005 -1.496 0.524 0.000 0.000 0.000 0.0860064007 36 -0.005 -1.496 0.509 0.000 0.000 0.000 0.0859274583 38 -0.005 -1.496 0.507 0.000 0.000 0.000 0.0859264095 48 -0.005 -1.496 0.507 -0.064 0.000 0.000 0.0855856668 49 -0.005 -1.496 0.507 -0.038 0.000 0.000 0.0849571324 59 -0.005 -1.496 0.507 -0.038 -0.082 0.000 0.0845974589 60 -0.005 -1.496 0.507 -0.038 -0.052 0.000 0.0843965611 61 -0.005 -1.496 0.507 -0.038 -0.051 0.000 0.0843894536 62 -0.005 -1.496 0.507 -0.038 -0.032 0.000 0.0843761775 63 -0.005 -1.496 0.507 -0.038 -0.040 0.000 0.0843609554 64 -0.005 -1.496 0.507 -0.038 -0.039 0.000 0.0843584762 65 -0.005 -1.496 0.507 -0.038 -0.037 0.000 0.0843576955 74 -0.005 -1.496 0.507 -0.038 -0.037 0.119 0.0818356881 76 -0.005 -1.496 0.507 -0.038 -0.037 0.104 0.0817269000 79 -0.005 -1.496 0.507 -0.038 -0.037 0.098 0.0817165227 89 0.062 -1.496 0.507 -0.038 -0.037 0.098 0.0784200867 91 0.079 -1.496 0.507 -0.038 -0.037 0.098 0.0783580601 92 0.076 -1.496 0.507 -0.038 -0.037 0.098 0.0783375078 93 0.074 -1.496 0.507 -0.038 -0.037 0.098 0.0783332821 102 0.074 -1.500 0.507 -0.038 -0.037 0.098 0.0782613848 104 0.074 -1.532 0.507 -0.038 -0.037 0.098 0.0782124181 105 0.074 -1.518 0.507 -0.038 -0.037 0.098 0.0781260750 106 0.074 -1.519 0.507 -0.038 -0.037 0.098 0.0781256759 114 0.074 -1.519 0.518 -0.038 -0.037 0.098 0.0780031421 116 0.074 -1.519 0.528 -0.038 -0.037 0.098 0.0779685306 117 0.074 -1.519 0.530 -0.038 -0.037 0.098 0.0779660198 128 0.074 -1.519 0.530 -0.079 -0.037 0.098 0.0775032375 129 0.074 -1.519 0.530 -0.070 -0.037 0.098 0.0773934281 130 0.074 -1.519 0.530 -0.066 -0.037 0.098 0.0773850494 140 0.074 -1.519 0.530 -0.066 -0.045 0.098 0.0772513331 142 0.074 -1.519 0.530 -0.066 -0.049 0.098 0.0772355263 151 0.074 -1.519 0.530 -0.066 -0.049 0.153 0.0768815185 152 0.074 -1.519 0.530 -0.066 -0.049 0.144 0.0767667536 153 0.074 -1.519 0.530 -0.066 -0.049 0.133 0.0767352155 154 0.074 -1.519 0.530 -0.066 -0.049 0.136 0.0767350124 156 0.074 -1.519 0.530 -0.066 -0.049 0.135 0.0767345098 157 0.153 -1.542 0.554 -0.094 -0.061 0.171 0.0757315281 165 0.156 -1.543 0.555 -0.096 -0.062 0.173 0.0757278872 166 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757259927 169 0.160 -1.544 0.556 -0.097 -0.062 0.175 0.0757256658 177 0.160 -1.544 0.556 -0.097 -0.062 0.204 0.0755171844 179 0.160 -1.544 0.556 -0.097 -0.062 0.196 0.0755028243 181 0.160 -1.544 0.556 -0.097 -0.062 0.199 0.0754996383 190 0.160 -1.513 0.556 -0.097 -0.062 0.199 0.0746624075 191 0.160 -1.464 0.556 -0.097 -0.062 0.199 0.0746055559 193 0.160 -1.487 0.556 -0.097 -0.062 0.199 0.0744588357 195 0.160 -1.489 0.556 -0.097 -0.062 0.199 0.0744576947 206 0.160 -1.489 0.566 -0.097 -0.062 0.199 0.0743555643 207 0.160 -1.489 0.571 -0.097 -0.062 0.199 0.0743416053 219 0.160 -1.489 0.571 -0.102 -0.062 0.199 0.0743244867 229 0.160 -1.489 0.571 -0.102 -0.054 0.199 0.0742840259 232 0.160 -1.489 0.571 -0.102 -0.055 0.199 0.0742834399 239 0.190 -1.498 0.580 -0.112 -0.059 0.213 0.0741403009 242 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741398050 244 0.209 -1.503 0.586 -0.119 -0.062 0.221 0.0741395840 247 0.211 -1.504 0.586 -0.120 -0.063 0.222 0.0741395027 248 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393948 249 0.210 -1.503 0.586 -0.120 -0.062 0.222 0.0741393463 259 0.210 -1.503 0.586 -0.120 -0.062 0.233 0.0738855742 261 0.210 -1.503 0.586 -0.120 -0.062 0.248 0.0737759217 262 0.210 -1.503 0.586 -0.120 -0.062 0.246 0.0737721810 273 0.210 -1.490 0.586 -0.120 -0.062 0.246 0.0736963995 285 0.210 -1.490 0.587 -0.120 -0.062 0.246 0.0736915133 286 0.210 -1.490 0.592 -0.120 -0.062 0.246 0.0736834938 288 0.210 -1.490 0.591 -0.120 -0.062 0.246 0.0736833623 298 0.210 -1.490 0.591 -0.111 -0.062 0.246 0.0735968226 300 0.210 -1.490 0.591 -0.107 -0.062 0.246 0.0735963327 302 0.210 -1.490 0.591 -0.108 -0.062 0.246 0.0735944569 303 0.210 -1.490 0.591 -0.109 -0.062 0.246 0.0735940538 311 0.210 -1.490 0.591 -0.109 -0.070 0.246 0.0735228430 312 0.210 -1.490 0.591 -0.109 -0.074 0.246 0.0735080376 315 0.210 -1.490 0.591 -0.109 -0.075 0.246 0.0735077031 321 0.240 -1.498 0.599 -0.120 -0.080 0.260 0.0734949468 322 0.226 -1.494 0.595 -0.115 -0.078 0.254 0.0734300529 324 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286940 327 0.228 -1.495 0.596 -0.116 -0.078 0.255 0.0734286205 338 0.228 -1.495 0.596 -0.116 -0.078 0.253 0.0734281123 348 0.228 -1.479 0.596 -0.116 -0.078 0.253 0.0734006223 349 0.228 -1.482 0.596 -0.116 -0.078 0.253 0.0733844990 350 0.228 -1.486 0.596 -0.116 -0.078 0.253 0.0733790100 362 0.228 -1.486 0.592 -0.116 -0.078 0.253 0.0733697099 364 0.228 -1.486 0.593 -0.116 -0.078 0.253 0.0733696556 374 0.228 -1.486 0.593 -0.110 -0.078 0.253 0.0733206040 376 0.228 -1.486 0.593 -0.105 -0.078 0.253 0.0733125478 377 0.228 -1.486 0.593 -0.107 -0.078 0.253 0.0733110118 387 0.228 -1.486 0.593 -0.107 -0.083 0.253 0.0732951888 396 0.232 -1.487 0.595 -0.108 -0.083 0.255 0.0732732502 397 0.237 -1.488 0.596 -0.110 -0.084 0.257 0.0732630673 398 0.238 -1.488 0.596 -0.110 -0.084 0.258 0.0732627839 399 0.238 -1.488 0.596 -0.110 -0.084 0.257 0.0732624241 403 0.247 -1.482 0.597 -0.104 -0.090 0.260 0.0732474931 437 0.238 -1.483 0.592 -0.110 -0.084 0.259 0.0732438122 439 0.238 -1.483 0.590 -0.110 -0.084 0.259 0.0732404503 449 0.238 -1.483 0.590 -0.108 -0.084 0.259 0.0732309201 451 0.238 -1.483 0.590 -0.105 -0.084 0.259 0.0732277520 452 0.238 -1.483 0.590 -0.106 -0.084 0.259 0.0732268628 462 0.238 -1.483 0.590 -0.106 -0.083 0.259 0.0732261879 471 0.241 -1.484 0.590 -0.107 -0.084 0.260 0.0732203038 472 0.242 -1.484 0.591 -0.108 -0.084 0.260 0.0732202274 481 0.245 -1.480 0.585 -0.105 -0.083 0.263 0.0732121668 527 0.242 -1.483 0.588 -0.105 -0.084 0.260 0.0732108126 547 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732097022 549 0.243 -1.483 0.589 -0.106 -0.084 0.261 0.0732096414 551 0.244 -1.482 0.587 -0.104 -0.084 0.262 0.0732042478 556 0.245 -1.481 0.586 -0.103 -0.084 0.262 0.0732030385 559 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029930 561 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029320 562 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732029164 564 0.245 -1.481 0.585 -0.103 -0.084 0.262 0.0732028100 577 0.245 -1.481 0.585 -0.103 -0.084 0.264 0.0732018670 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.013482 1 -25.0 -25.0 25.0 1.015559 2 -25.0 25.0 -25.0 1.034208 3 -25.0 25.0 25.0 1.000666 4 25.0 -25.0 -25.0 1.034182 5 25.0 -25.0 25.0 0.991798 6 25.0 25.0 -25.0 1.006023 7 25.0 25.0 25.0 1.034180 REL: 8 0.073202 8.130098 1.016262 rel = 0.0720305 Number of iterations 7 Min cost was 0.073202 Number of FunctionCalls 641 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 2.591000 sec Parameters at optimum (transmm) 0.24532 -1.48124 0.58539 Parameters at optimum (rotdeg) -0.10298 -0.08425 0.26413 Final costs ---------------- Number of surface hits 3238 WM Intensity 60.0746 +/- 10.5131 Ctx Intensity 78.1624 +/- 10.7433 Pct Contrast 26.4330 +/- 15.2985 Cost 0.0732 RelCost 0.3170 Reg at min cost was 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat, type = 14 Original Reg 0.999 -0.039 -0.025 0.009; 0.020 -0.121 0.992 1.308; -0.042 -0.992 -0.120 -0.930; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.002 0.004 -0.241; -0.005 0.002 0.000 1.483; -0.001 -0.000 0.002 -0.583; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.655014 Computing change in rh position Surface RMS Diff (mm) 1.549561 1.872015 mri_segreg done mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ setenv SUBJECTS_DIR /home/data/exppsy/forrest_gump/openfmri.org/freesurfer cd /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/scripts mri_segreg --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii --init-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat --out-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.mincost --dof 6 --nmax 36 --param /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat.param --surf white --cur-reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname snake5 machine x86_64 user fkaule movvol /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/template.nii regfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/tmp.bbregister.19132/bbr.pass1.dat subject sub006 dof 6 outregfile /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.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 1376539157 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 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 1.000144 1 -25.0 -25.0 25.0 1.011963 2 -25.0 25.0 -25.0 1.028762 3 -25.0 25.0 25.0 1.017444 4 25.0 -25.0 -25.0 1.023030 5 25.0 -25.0 25.0 1.003200 6 25.0 25.0 -25.0 1.006099 7 25.0 25.0 25.0 1.018704 REL: 8 0.074000 8.109344 1.013668 rel = 0.0730019 Initial costs ---------------- Number of surface hits 323295 WM Intensity 60.0945 +/- 10.4129 Ctx Intensity 78.3960 +/- 10.7337 Pct Contrast 26.6644 +/- 15.2882 Cost 0.0740 RelCost 0.0730 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0884 0.0884 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0860 0.0860 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.0824 0.0824 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0789 0.0789 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.0775 0.0775 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0762 0.0762 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0755 0.0755 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0755 0.0755 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0732 0.0732 0.0 Brute Force -------------------------- Min cost was 0.073202 Number of iterations 729 Search time 2.842000 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 -0.011 0.000 0.000 0.000 0.000 0.000 0.0739579968 8 -0.023 0.000 0.000 0.000 0.000 0.000 0.0739393766 10 -0.024 0.000 0.000 0.000 0.000 0.000 0.0739391684 18 -0.024 0.068 0.000 0.000 0.000 0.000 0.0736410288 19 -0.024 0.054 0.000 0.000 0.000 0.000 0.0736210929 28 -0.024 0.054 0.144 0.000 0.000 0.000 0.0712034427 29 -0.024 0.054 0.145 0.000 0.000 0.000 0.0712014029 30 -0.024 0.054 0.154 0.000 0.000 0.000 0.0711957153 32 -0.024 0.054 0.152 0.000 0.000 0.000 0.0711948811 42 -0.024 0.054 0.152 0.003 0.000 0.000 0.0711937157 51 -0.024 0.054 0.152 0.003 -0.021 0.000 0.0710840807 52 -0.024 0.054 0.152 0.003 -0.028 0.000 0.0710745386 55 -0.024 0.054 0.152 0.003 -0.029 0.000 0.0710742340 63 -0.024 0.054 0.152 0.003 -0.029 0.003 0.0710718816 65 -0.024 0.054 0.152 0.003 -0.029 0.005 0.0710714752 66 -0.024 0.054 0.152 0.003 -0.029 0.006 0.0710712416 77 -0.013 0.054 0.152 0.003 -0.029 0.006 0.0710605916 87 -0.013 0.055 0.152 0.003 -0.029 0.006 0.0710605245 96 -0.013 0.055 0.154 0.003 -0.029 0.006 0.0710602217 106 -0.013 0.055 0.154 0.004 -0.029 0.006 0.0710595122 115 -0.013 0.055 0.154 0.004 -0.031 0.006 0.0710593576 124 -0.013 0.055 0.154 0.004 -0.031 0.010 0.0710563353 126 -0.013 0.055 0.154 0.004 -0.031 0.011 0.0710561702 127 -0.013 0.055 0.154 0.004 -0.031 0.012 0.0710560869 130 -0.003 0.056 0.156 0.006 -0.032 0.018 0.0710552827 136 -0.007 0.056 0.155 0.005 -0.032 0.016 0.0710535106 137 -0.008 0.056 0.155 0.005 -0.031 0.015 0.0710534580 138 -0.008 0.056 0.155 0.005 -0.031 0.016 0.0710533858 162 -0.008 0.057 0.155 0.005 -0.031 0.016 0.0710532018 171 -0.008 0.057 0.152 0.005 -0.031 0.016 0.0710519125 198 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517517 199 -0.006 0.057 0.153 0.005 -0.032 0.016 0.0710517061 200 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710517012 203 -0.007 0.057 0.152 0.005 -0.032 0.016 0.0710516797 217 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516335 270 -0.007 0.057 0.152 0.005 -0.032 0.017 0.0710516217 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.000527 1 -25.0 -25.0 25.0 1.012389 2 -25.0 25.0 -25.0 1.028572 3 -25.0 25.0 25.0 1.018441 4 25.0 -25.0 -25.0 1.022629 5 25.0 -25.0 25.0 1.001609 6 25.0 25.0 -25.0 1.005235 7 25.0 25.0 25.0 1.020102 REL: 8 0.071052 8.109503 1.013688 rel = 0.0700922 Number of iterations 4 Min cost was 0.071052 Number of FunctionCalls 333 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 51.287000 sec Parameters at optimum (transmm) -0.00683 0.05697 0.15243 Parameters at optimum (rotdeg) 0.00519 -0.03151 0.01697 Final costs ---------------- Number of surface hits 323295 WM Intensity 60.0684 +/- 10.3946 Ctx Intensity 78.3842 +/- 10.7444 Pct Contrast 26.6871 +/- 15.2674 Cost 0.0711 RelCost 0.0730 Reg at min cost was 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; Writing optimal reg to /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat, type = 14 Original Reg 0.999 -0.037 -0.029 0.250; 0.024 -0.123 0.992 -0.175; -0.040 -0.992 -0.122 -0.347; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.000 0.007; -0.000 -0.000 -0.000 -0.057; -0.001 0.000 -0.000 -0.153; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.153461 Computing change in rh position Surface RMS Diff (mm) 0.170445 0.209095 mri_segreg done tkregister2_cmdl --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --noedit --ltaout /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.lta tkregister_tcl /opt/freesurfer/5.3.0/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz reg file /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.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 -------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz Tmov: -------------------- -0.700 0.000 0.000 95.889; 0.000 0.000 0.667 -128.000; 0.000 -0.667 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; Determinant 1 subject = sub006 RegMat --------------------------- 0.999 -0.036 -0.029 0.243; 0.025 -0.123 0.992 -0.118; -0.040 -0.992 -0.122 -0.195; 0.000 0.000 0.000 1.000; transformed matrix: 1.000 -0.005 0.001 -0.130; 0.005 1.000 0.005 -0.080; -0.001 -0.005 1.000 0.196; 0.000 0.000 0.000 1.000; transformed matrix: 0.699 -0.026 -0.016 40.677; -0.021 -0.081 -0.661 273.305; 0.025 0.661 -0.082 13.122; 0.000 0.000 0.000 1.000; Cleaning up Started at Thu Aug 8 23:20:09 CEST 2013 Ended at Thu Aug 8 23:33:28 CEST 2013 BBR-Run-Time-Sec 799 bbregister Done To check results, run: tkregister2 --mov /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/orig/T2raw.mgz --reg /home/data/exppsy/forrest_gump/openfmri.org/freesurfer/sub006/mri/transforms/T2raw.dat --surf