Logfile for bbregister Wed Apr 24 21:19:18 EDT 2013 setenv SUBJECTS_DIR /autofs/space/terrier_002/users/nicks/subjects/nicks_recons cd /homes/10/ayendiki /usr/local/freesurfer/dev/bin/bbregister --s nick-2005-09-05 --init-fsl --dti --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat --fslmat /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/diff2anatorig.bbr.mat $Id: bbregister,v 1.56 2013/03/25 18:04:29 greve Exp $ Linux compute-0-3 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_convert /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii mri_convert /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii $Id: mri_convert.c,v 1.203 2012/12/06 21:44:17 greve Exp $ reading from /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999701, 0.0244268, 0.000465598) j_ras = (0.023757, 0.976382, -0.21474) k_ras = (0.0057, 0.214665, 0.976671) writing to /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii... fslregister --s nick-2005-09-05 --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --niters 1 --maxangle 90 --tmp /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat.fslregister.log Wed Apr 24 21:19:53 EDT 2013 --s nick-2005-09-05 --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --niters 1 --maxangle 90 --tmp /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov $Id: fslregister,v 1.36 2012/11/08 16:18:43 greve Exp $ compute-0-3 Linux compute-0-3 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /homes/10/ayendiki mri_convert /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/mri/brainmask.mgz /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/refvol.fslregister.nii mri_convert /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/mri/brainmask.mgz /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.203 2012/12/06 21:44:17 greve Exp $ reading from /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 6.33299e-08, -2.04891e-08) j_ras = (-9.31323e-09, 2.32831e-10, -1) k_ras = (7.07805e-08, 1, 1.74623e-09) writing to /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/refvol.fslregister.nii... -------------------------------------- /homes/10/ayendiki mri_convert /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii --frame 0 mri_convert /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.203 2012/12/06 21:44:17 greve Exp $ reading from /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999701, 0.0244268, 0.000465598) j_ras = (0.023757, 0.976382, -0.21474) k_ras = (0.0057, 0.214665, 0.976671) keeping frame 0 writing to /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii... Mov determinant is -8 /homes/10/ayendiki tkregister2_cmdl --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/reg0.11859.dat --regheader --fslregout /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat.fsl.mat0 --s nick-2005-09-05 --noedit tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii reg file /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/reg0.11859.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.126 2012/01/20 21:00:37 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/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 /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -60.000; 0.000 -2.000 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) -------- 1.000 -0.024 -0.000 3.118; 0.006 0.215 0.977 2.259; -0.024 -0.976 0.215 -1.164; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.024 -0.000 3.118; 0.006 0.215 0.977 2.259; -0.024 -0.976 0.215 -1.164; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2005-09-05 RegMat --------------------------- 1.000 -0.024 -0.000 3.118; 0.006 0.215 0.977 2.259; -0.024 -0.976 0.215 -1.164; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Wed Apr 24 21:20:20 EDT 2013 /homes/10/ayendiki flirt.fsl -ref /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/refvol.fslregister.nii -in /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/current/etc/flirtsch/xyztrans.sch -init /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat.fsl.mat0 Wed Apr 24 21:20:40 EDT 2013 /homes/10/ayendiki flirt.fsl -ref /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/refvol.fslregister.nii -in /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat.fsl.mat -init /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/dev/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s nick-2005-09-05 --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --fslreg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 -0.041 0.002 8.031; 0.011 0.235 -0.972 154.415; 0.039 0.971 0.235 -17.038; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii reg file /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.126 2012/01/20 21:00:37 greve Exp $ Diagnostic Level -1 INFO: loading target /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/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 /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -60.000; 0.000 -2.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -8, ref det = -1 ---- Input registration matrix (computed) -------- 0.999 -0.039 0.011 2.750; -0.002 0.235 0.972 -0.065; -0.041 -0.971 0.235 -1.795; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 -0.039 0.011 2.750; -0.002 0.235 0.972 -0.065; -0.041 -0.971 0.235 -1.795; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2005-09-05 RegMat --------------------------- 0.999 -0.039 0.011 2.750; -0.002 0.235 0.972 -0.065; -0.041 -0.971 0.235 -1.795; 0.000 0.000 0.000 1.000; (standard_in) 1: Error: multiple letter name - nick (standard_in) 2: Error: comparison in expression Started at Wed Apr 24 21:19:53 EDT 2013 Ended at Wed Apr 24 21:21:16 EDT 2013 fslregister Done To check results, run: tkregister2 --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --surf orig mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/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 1.105 2011/10/27 18:36:43 greve Exp $ setenv SUBJECTS_DIR /autofs/space/terrier_002/users/nicks/subjects/nicks_recons cd /autofs/homes/010/ayendiki mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/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 compute-0-3 machine x86_64 user ayendiki movvol /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii regfile /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.init.dat subject nick-2005-09-05 dof 6 outregfile /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/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 1366963296 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 0.011 2.750; -0.002 0.235 0.972 -0.065; -0.041 -0.971 0.235 -1.795; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 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 Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.985268 1 -25.0 -25.0 25.0 1.001482 2 -25.0 25.0 -25.0 0.982003 3 -25.0 25.0 25.0 1.008824 4 25.0 -25.0 -25.0 0.996099 5 25.0 -25.0 25.0 1.011423 6 25.0 25.0 -25.0 0.981698 7 25.0 25.0 25.0 1.018598 REL: 8 0.479159 7.985394 0.998174 rel = 0.480035 Initial costs ---------------- Number of surface hits 2679 WM Intensity 208.2156 +/- 115.4473 Ctx Intensity 275.5323 +/- 149.1829 Pct Contrast 23.8271 +/- 42.4135 Cost 0.4792 RelCost 0.4800 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9894 0.9894 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9605 0.9605 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9387 0.9387 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9214 0.9214 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8550 0.8550 0.0 97 -4.0000 0.0000 -4.0000 0.0000 4.0000 0.0000 0.8201 0.8201 0.0 123 -4.0000 0.0000 0.0000 0.0000 4.0000 -4.0000 0.7799 0.7799 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7612 0.7612 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7145 0.7145 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4792 0.4792 0.0 Brute Force -------------------------- Min cost was 0.479159 Number of iterations 729 Search time 2.789000 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 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0 7 0.094 0.000 0.000 0.000 0.000 0.000 0.4773978059 9 0.082 0.000 0.000 0.000 0.000 0.000 0.4772499349 11 0.079 0.000 0.000 0.000 0.000 0.000 0.4772340561 13 0.077 0.000 0.000 0.000 0.000 0.000 0.4772304432 14 0.076 0.000 0.000 0.000 0.000 0.000 0.4772302793 27 0.076 -0.017 0.000 0.000 0.000 0.000 0.4771646253 28 0.076 -0.011 0.000 0.000 0.000 0.000 0.4771369853 32 0.076 -0.011 1.000 0.000 0.000 0.000 0.4668070762 41 0.076 -0.011 1.034 0.000 0.000 0.000 0.4661634835 49 0.076 -0.011 1.034 -0.618 0.000 0.000 0.4653729260 51 0.076 -0.011 1.034 -0.319 0.000 0.000 0.4607439548 52 0.076 -0.011 1.034 -0.321 0.000 0.000 0.4607336043 53 0.076 -0.011 1.034 -0.359 0.000 0.000 0.4604278046 55 0.076 -0.011 1.034 -0.402 0.000 0.000 0.4600394552 56 0.076 -0.011 1.034 -0.406 0.000 0.000 0.4598766710 57 0.076 -0.011 1.034 -0.426 0.000 0.000 0.4596078451 58 0.076 -0.011 1.034 -0.423 0.000 0.000 0.4595674694 59 0.076 -0.011 1.034 -0.420 0.000 0.000 0.4595472926 61 0.076 -0.011 1.034 -0.419 0.000 0.000 0.4595468171 71 0.076 -0.011 1.034 -0.419 -0.013 0.000 0.4595254976 72 0.076 -0.011 1.034 -0.419 -0.012 0.000 0.4595192497 73 0.076 -0.011 1.034 -0.419 -0.008 0.000 0.4595102351 85 0.076 -0.011 1.034 -0.419 -0.008 -0.023 0.4592383690 powell nthiter 1 96 -0.045 -0.011 1.034 -0.419 -0.008 -0.023 0.4567254201 98 -0.049 -0.011 1.034 -0.419 -0.008 -0.023 0.4567064497 99 -0.055 -0.011 1.034 -0.419 -0.008 -0.023 0.4566928111 100 -0.057 -0.011 1.034 -0.419 -0.008 -0.023 0.4566914905 101 -0.058 -0.011 1.034 -0.419 -0.008 -0.023 0.4566911867 102 -0.059 -0.011 1.034 -0.419 -0.008 -0.023 0.4566911059 108 -0.059 -0.629 1.034 -0.419 -0.008 -0.023 0.4501740042 110 -0.059 -0.433 1.034 -0.419 -0.008 -0.023 0.4430522877 111 -0.059 -0.368 1.034 -0.419 -0.008 -0.023 0.4421722856 113 -0.059 -0.378 1.034 -0.419 -0.008 -0.023 0.4421560909 114 -0.059 -0.375 1.034 -0.419 -0.008 -0.023 0.4421504952 115 -0.059 -0.374 1.034 -0.419 -0.008 -0.023 0.4421502751 125 -0.059 -0.374 0.944 -0.419 -0.008 -0.023 0.4399549576 127 -0.059 -0.374 0.968 -0.419 -0.008 -0.023 0.4394458655 129 -0.059 -0.374 0.969 -0.419 -0.008 -0.023 0.4394454388 140 -0.059 -0.374 0.969 -0.406 -0.008 -0.023 0.4394397527 141 -0.059 -0.374 0.969 -0.412 -0.008 -0.023 0.4394104173 152 -0.059 -0.374 0.969 -0.412 -0.009 -0.023 0.4394079702 153 -0.059 -0.374 0.969 -0.412 -0.010 -0.023 0.4394074665 166 -0.059 -0.374 0.969 -0.412 -0.010 -0.025 0.4394041568 powell nthiter 2 190 -0.059 -0.379 0.969 -0.412 -0.010 -0.025 0.4393859360 203 -0.059 -0.379 0.966 -0.412 -0.010 -0.025 0.4393780669 217 -0.059 -0.379 0.966 -0.411 -0.010 -0.025 0.4393760796 218 -0.059 -0.379 0.966 -0.410 -0.010 -0.025 0.4393759200 229 -0.059 -0.379 0.966 -0.410 -0.009 -0.025 0.4393755719 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 0.981354 1 -25.0 -25.0 25.0 1.000527 2 -25.0 25.0 -25.0 0.994936 3 -25.0 25.0 25.0 1.001068 4 25.0 -25.0 -25.0 1.009771 5 25.0 -25.0 25.0 1.017197 6 25.0 25.0 -25.0 0.997246 7 25.0 25.0 25.0 1.026224 REL: 8 0.439376 8.028324 1.003541 rel = 0.437825 Number of iterations 2 Min cost was 0.439376 Number of FunctionCalls 241 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.985000 sec Parameters at optimum (transmm) -0.05920 -0.37927 0.96597 Parameters at optimum (rotdeg) -0.41032 -0.00897 -0.02470 Final costs ---------------- Number of surface hits 2680 WM Intensity 204.6694 +/- 112.1848 Ctx Intensity 275.3230 +/- 147.4957 Pct Contrast 25.6131 +/- 41.7755 Cost 0.4394 RelCost 0.4800 Reg at min cost was 0.999 -0.039 0.011 2.691; -0.002 0.228 0.974 -0.458; -0.040 -0.973 0.228 -0.828; 0.000 0.000 0.000 1.000; Writing optimal reg to /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/bbr.pass1.dat, type = 14 Original Reg 0.999 -0.039 0.011 2.750; -0.002 0.235 0.972 -0.065; -0.041 -0.971 0.235 -1.795; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.000 -0.000 0.059; 0.001 0.007 -0.002 0.393; -0.000 0.002 0.007 -0.967; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.010890 Computing change in rh position Surface RMS Diff (mm) 1.010808 1.369522 mri_segreg done mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/bbr.pass1.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.105 2011/10/27 18:36:43 greve Exp $ setenv SUBJECTS_DIR /autofs/space/terrier_002/users/nicks/subjects/nicks_recons cd /autofs/homes/010/ayendiki mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/bbr.pass1.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname compute-0-3 machine x86_64 user ayendiki movvol /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/template.nii regfile /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/tmp.bbregister.11542/bbr.pass1.dat subject nick-2005-09-05 dof 6 outregfile /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.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 1367454685 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 0.011 2.691; -0.002 0.228 0.974 -0.458; -0.040 -0.973 0.228 -0.828; 0.000 0.000 0.000 1.000; Loading mov Extracting frame 0 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 Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.994426 1 -25.0 -25.0 25.0 1.009215 2 -25.0 25.0 -25.0 1.028122 3 -25.0 25.0 25.0 0.993302 4 25.0 -25.0 -25.0 1.009181 5 25.0 -25.0 25.0 1.005755 6 25.0 25.0 -25.0 0.984185 7 25.0 25.0 25.0 1.020685 REL: 8 0.457067 8.044872 1.005609 rel = 0.454518 Initial costs ---------------- Number of surface hits 267146 WM Intensity 206.3329 +/- 113.7101 Ctx Intensity 277.7079 +/- 152.6916 Pct Contrast 25.3842 +/- 42.7198 Cost 0.4571 RelCost 0.4545 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.4511 0.4511 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.4495 0.4495 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.4494 0.4494 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.4464 0.4464 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.4459 0.4459 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.4453 0.4453 0.0 21 -0.1000 -0.1000 -0.1000 0.1000 0.0000 -0.1000 0.4450 0.4450 0.0 24 -0.1000 -0.1000 -0.1000 0.1000 0.1000 -0.1000 0.4444 0.4444 0.0 36 -0.1000 -0.1000 0.0000 0.0000 -0.1000 -0.1000 0.4434 0.4434 0.0 54 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 -0.1000 0.4425 0.4425 0.0 63 -0.1000 -0.1000 0.1000 0.0000 -0.1000 -0.1000 0.4412 0.4412 0.0 258 0.0000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.4408 0.4408 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.4399 0.4399 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.4394 0.4394 0.0 606 0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.4393 0.4393 0.0 Brute Force -------------------------- Min cost was 0.439324 Number of iterations 729 Search time 1.404000 sec Parameters at best (transmm, rotdeg) 0.100 0.000 0.000 0.000 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0 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 9 0.095 0.000 0.000 0.000 0.000 -0.100 0.4542020223 10 0.096 0.000 0.000 0.000 0.000 -0.100 0.4542017370 18 0.096 -0.119 0.000 0.000 0.000 -0.100 0.4536342069 19 0.096 -0.104 0.000 0.000 0.000 -0.100 0.4535822687 20 0.096 -0.089 0.000 0.000 0.000 -0.100 0.4535558512 22 0.096 -0.090 0.000 0.000 0.000 -0.100 0.4535537768 25 0.096 -0.091 0.000 0.000 0.000 -0.100 0.4535528556 32 0.096 -0.091 -0.031 0.000 0.000 -0.100 0.4535116466 34 0.096 -0.091 -0.027 0.000 0.000 -0.100 0.4535109015 43 0.096 -0.091 -0.027 -0.081 0.000 -0.100 0.4533216331 44 0.096 -0.091 -0.027 -0.067 0.000 -0.100 0.4532858731 45 0.096 -0.091 -0.027 -0.056 0.000 -0.100 0.4532792536 46 0.096 -0.091 -0.027 -0.058 0.000 -0.100 0.4532772389 55 0.096 -0.091 -0.027 -0.058 -0.018 -0.100 0.4531727268 58 0.096 -0.091 -0.027 -0.058 -0.032 -0.100 0.4531453925 60 0.096 -0.091 -0.027 -0.058 -0.031 -0.100 0.4531453258 69 0.096 -0.091 -0.027 -0.058 -0.031 -0.315 0.4515692971 70 0.096 -0.091 -0.027 -0.058 -0.031 -0.308 0.4515495675 71 0.096 -0.091 -0.027 -0.058 -0.031 -0.284 0.4515342067 74 0.096 -0.091 -0.027 -0.058 -0.031 -0.279 0.4515332344 78 0.096 -0.091 -0.027 -0.058 -0.031 -0.281 0.4515311752 powell nthiter 1 87 0.088 -0.091 -0.027 -0.058 -0.031 -0.281 0.4514826416 89 0.056 -0.091 -0.027 -0.058 -0.031 -0.281 0.4514211147 90 0.063 -0.091 -0.027 -0.058 -0.031 -0.281 0.4514171324 99 0.063 -0.153 -0.027 -0.058 -0.031 -0.281 0.4512252898 103 0.063 -0.163 -0.027 -0.058 -0.031 -0.281 0.4512140417 104 0.063 -0.170 -0.027 -0.058 -0.031 -0.281 0.4512116765 114 0.063 -0.170 -0.026 -0.058 -0.031 -0.281 0.4512066311 115 0.063 -0.170 0.016 -0.058 -0.031 -0.281 0.4511693550 117 0.063 -0.170 0.005 -0.058 -0.031 -0.281 0.4511654081 122 0.063 -0.170 0.004 -0.058 -0.031 -0.281 0.4511653562 130 0.063 -0.170 0.004 -0.099 -0.031 -0.281 0.4510502825 133 0.063 -0.170 0.004 -0.097 -0.031 -0.281 0.4510491064 134 0.063 -0.170 0.004 -0.096 -0.031 -0.281 0.4510488123 142 0.063 -0.170 0.004 -0.096 0.011 -0.281 0.4509453364 144 0.063 -0.170 0.004 -0.096 0.008 -0.281 0.4509453358 146 0.063 -0.170 0.004 -0.096 0.009 -0.281 0.4509452793 154 0.063 -0.170 0.004 -0.096 0.009 -0.307 0.4509248140 155 0.063 -0.170 0.004 -0.096 0.009 -0.304 0.4509233164 156 0.063 -0.170 0.004 -0.096 0.009 -0.301 0.4509225664 157 0.063 -0.170 0.004 -0.096 0.009 -0.300 0.4509222524 159 0.063 -0.170 0.004 -0.096 0.009 -0.297 0.4509221531 161 0.063 -0.170 0.004 -0.096 0.009 -0.298 0.4509220315 powell nthiter 2 169 0.062 -0.170 0.004 -0.096 0.009 -0.298 0.4509198028 170 0.036 -0.170 0.004 -0.096 0.009 -0.298 0.4508739250 173 0.020 -0.170 0.004 -0.096 0.009 -0.298 0.4508641958 175 0.024 -0.170 0.004 -0.096 0.009 -0.298 0.4508633837 177 0.023 -0.170 0.004 -0.096 0.009 -0.298 0.4508633557 185 0.023 -0.167 0.004 -0.096 0.009 -0.298 0.4508605646 198 0.023 -0.167 0.022 -0.096 0.009 -0.298 0.4508355484 223 0.023 -0.167 0.022 -0.096 0.008 -0.298 0.4508346884 232 0.023 -0.167 0.022 -0.096 0.008 -0.334 0.4507780924 235 0.023 -0.167 0.022 -0.096 0.008 -0.341 0.4507747474 237 0.023 -0.167 0.022 -0.096 0.008 -0.343 0.4507746116 powell nthiter 3 249 0.014 -0.167 0.022 -0.096 0.008 -0.343 0.4507669546 250 0.015 -0.167 0.022 -0.096 0.008 -0.343 0.4507667538 251 0.016 -0.167 0.022 -0.096 0.008 -0.343 0.4507667138 261 0.016 -0.177 0.022 -0.096 0.008 -0.343 0.4507640394 266 0.016 -0.178 0.022 -0.096 0.008 -0.343 0.4507633197 267 0.016 -0.181 0.022 -0.096 0.008 -0.343 0.4507628989 277 0.016 -0.180 0.020 -0.096 0.008 -0.343 0.4507589655 278 0.016 -0.180 0.012 -0.096 0.008 -0.343 0.4507523497 280 0.016 -0.180 0.011 -0.096 0.008 -0.343 0.4507523040 297 0.016 -0.180 0.011 -0.096 0.038 -0.343 0.4507475046 298 0.016 -0.180 0.011 -0.096 0.025 -0.343 0.4507314621 299 0.016 -0.180 0.011 -0.096 0.024 -0.343 0.4507312000 300 0.016 -0.180 0.011 -0.096 0.023 -0.343 0.4507311405 301 0.016 -0.180 0.011 -0.096 0.022 -0.343 0.4507310826 312 0.016 -0.180 0.011 -0.096 0.022 -0.344 0.4507307729 313 0.016 -0.180 0.011 -0.096 0.022 -0.346 0.4507307165 powell nthiter 4 326 0.013 -0.180 0.011 -0.096 0.022 -0.345 0.4507291377 327 0.012 -0.180 0.011 -0.096 0.022 -0.345 0.4507290778 336 0.012 -0.174 0.011 -0.096 0.022 -0.345 0.4507273753 348 0.012 -0.174 0.014 -0.096 0.022 -0.345 0.4507264151 358 0.012 -0.174 0.014 -0.094 0.022 -0.345 0.4507260791 368 0.012 -0.174 0.014 -0.094 0.026 -0.345 0.4507250694 378 0.012 -0.174 0.014 -0.094 0.026 -0.347 0.4507246137 379 0.012 -0.174 0.014 -0.094 0.026 -0.348 0.4507243401 powell nthiter 5 392 0.011 -0.174 0.014 -0.094 0.026 -0.348 0.4507243081 402 0.011 -0.172 0.014 -0.094 0.026 -0.348 0.4507225628 404 0.011 -0.173 0.014 -0.094 0.026 -0.348 0.4507187853 433 0.011 -0.173 0.014 -0.094 0.025 -0.348 0.4507187746 446 0.011 -0.173 0.014 -0.094 0.025 -0.350 0.4507186665 456 0.011 -0.173 0.014 -0.094 0.025 -0.349 0.4507186181 459 0.011 -0.173 0.014 -0.094 0.025 -0.349 0.4507185599 461 0.011 -0.173 0.014 -0.094 0.025 -0.349 0.4507184903 463 0.011 -0.173 0.014 -0.094 0.025 -0.349 0.4507184819 powell nthiter 6 Powell done niters = 6 Computing relative cost 0 -25.0 -25.0 -25.0 0.993126 1 -25.0 -25.0 25.0 1.009772 2 -25.0 25.0 -25.0 1.031154 3 -25.0 25.0 25.0 0.987809 4 25.0 -25.0 -25.0 1.008500 5 25.0 -25.0 25.0 1.005232 6 25.0 25.0 -25.0 0.987331 7 25.0 25.0 25.0 1.021885 REL: 8 0.450719 8.044810 1.005601 rel = 0.448208 Number of iterations 6 Min cost was 0.450719 Number of FunctionCalls 538 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 86.033000 sec Parameters at optimum (transmm) 0.01133 -0.17311 0.01313 Parameters at optimum (rotdeg) -0.09412 0.02482 -0.34942 Final costs ---------------- Number of surface hits 267254 WM Intensity 205.3518 +/- 114.1151 Ctx Intensity 276.3862 +/- 150.8906 Pct Contrast 25.5341 +/- 42.4991 Cost 0.4507 RelCost 0.4545 Reg at min cost was 0.999 -0.038 0.018 2.699; -0.008 0.227 0.974 -0.649; -0.041 -0.973 0.226 -0.815; 0.000 0.000 0.000 1.000; Writing optimal reg to /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.999 -0.039 0.011 2.691; -0.002 0.228 0.974 -0.458; -0.040 -0.973 0.228 -0.828; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.001 -0.006 -0.008; 0.006 0.001 -0.000 0.191; 0.000 0.000 0.002 -0.013; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.190675 Computing change in rh position Surface RMS Diff (mm) 0.286107 0.580246 mri_segreg done tkregister2_cmdl --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/diff2anatorig.bbr.mat tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz reg file /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.126 2012/01/20 21:00:37 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- 0.999 -0.038 0.018 2.699; -0.008 0.227 0.974 -0.649; -0.041 -0.973 0.226 -0.815; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2005-09-05/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 /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -60.000; 0.000 -2.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.999 -0.038 0.018 2.699; -0.008 0.227 0.974 -0.649; -0.041 -0.973 0.226 -0.815; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2005-09-05 RegMat --------------------------- 0.999 -0.038 0.018 2.699; -0.008 0.227 0.974 -0.649; -0.041 -0.973 0.226 -0.815; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -8, ref det = -1 Cleaning up Started at Wed Apr 24 21:19:18 EDT 2013 Ended at Wed Apr 24 21:23:43 EDT 2013 BBR-Run-Time-Sec 265 bbregister Done To check results, run: tkregister2 --mov /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2005-09-05/dmri/xfms/anatorig2diff.bbr.dat --surf