Logfile for bbregister Wed Apr 24 21:24:18 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-2012-12-18 --init-fsl --dti --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat --fslmat /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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-2012-12-18/dmri/dwi.nii.gz /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii mri_convert /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/dwi.nii.gz /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) writing to /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii... fslregister --s nick-2012-12-18 --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --niters 1 --maxangle 90 --tmp /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat.fslregister.log Wed Apr 24 21:25:16 EDT 2013 --s nick-2012-12-18 --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --niters 1 --maxangle 90 --tmp /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/mri/brainmask.mgz /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/refvol.fslregister.nii mri_convert /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2012-12-18/mri/brainmask.mgz /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/mri/brainmask.mgz... TR=2530.00, TE=1.74, TI=-1.00, flip angle=7.00 i_ras = (-1, -1.30385e-07, 8.9407e-08) j_ras = (1.08499e-07, 2.22353e-08, -1) k_ras = (-5.96046e-08, 1, -1.39989e-08) writing to /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/refvol.fslregister.nii... -------------------------------------- /homes/10/ayendiki mri_convert /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/movvol.fslregister.nii --frame 0 mri_convert /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999278, -0.0375823, -0.00564044) j_ras = (-0.0367492, 0.917788, 0.395367) k_ras = (0.00968205, -0.395289, 0.918506) keeping frame 0 writing to /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/movvol.fslregister.nii... Mov determinant is -8 /homes/10/ayendiki tkregister2_cmdl --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/movvol.fslregister.nii --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/reg0.14966.dat --regheader --fslregout /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat.fsl.mat0 --s nick-2012-12-18 --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-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/movvol.fslregister.nii reg file /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/reg0.14966.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-2012-12-18/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/movvol.fslregister.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -64.000; 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) -------- 0.999 0.038 0.006 -0.502; 0.010 -0.395 0.919 -30.684; 0.037 -0.918 -0.395 3.327; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 0.038 0.006 -0.502; 0.010 -0.395 0.919 -30.684; 0.037 -0.918 -0.395 3.327; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2012-12-18 RegMat --------------------------- 0.999 0.038 0.006 -0.502; 0.010 -0.395 0.919 -30.684; 0.037 -0.918 -0.395 3.327; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -8, ref det = -1 Wed Apr 24 21:25:29 EDT 2013 /homes/10/ayendiki flirt.fsl -ref /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/refvol.fslregister.nii -in /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/current/etc/flirtsch/xyztrans.sch -init /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat.fsl.mat0 Wed Apr 24 21:25:50 EDT 2013 /homes/10/ayendiki flirt.fsl -ref /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/refvol.fslregister.nii -in /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat.fsl.mat -init /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/dev/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s nick-2012-12-18 --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --fslreg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat.fsl.mat --noedit tkregister_tcl /usr/local/freesurfer/dev/tktools/tkregister2.tcl ---- FSL registration matrix -------- 0.999 0.040 -0.004 -4.896; 0.011 -0.367 -0.930 202.198; -0.038 0.930 -0.367 27.370; 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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii reg file /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -64.000; 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 0.038 0.011 -0.135; 0.004 -0.367 0.930 -32.387; 0.040 -0.930 -0.367 2.004; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.999 0.038 0.011 -0.135; 0.004 -0.367 0.930 -32.387; 0.040 -0.930 -0.367 2.004; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2012-12-18 RegMat --------------------------- 0.999 0.038 0.011 -0.135; 0.004 -0.367 0.930 -32.387; 0.040 -0.930 -0.367 2.004; 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 21:25:17 EDT 2013 Ended at Wed Apr 24 21:26:26 EDT 2013 fslregister Done To check results, run: tkregister2 --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --surf orig mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii regfile /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/reg.init.dat subject nick-2012-12-18 dof 6 outregfile /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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 1367295083 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.999 0.038 0.011 -0.135; 0.004 -0.367 0.930 -32.387; 0.040 -0.930 -0.367 2.004; 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 1.002704 1 -25.0 -25.0 25.0 1.017829 2 -25.0 25.0 -25.0 1.003894 3 -25.0 25.0 25.0 0.977542 4 25.0 -25.0 -25.0 1.002915 5 25.0 -25.0 25.0 0.996731 6 25.0 25.0 -25.0 1.027332 7 25.0 25.0 25.0 1.045094 REL: 8 0.311583 8.074042 1.009255 rel = 0.308726 Initial costs ---------------- Number of surface hits 2735 WM Intensity 238.5029 +/- 66.1667 Ctx Intensity 314.0423 +/- 95.9477 Pct Contrast 25.8692 +/- 27.7436 Cost 0.3116 RelCost 0.3087 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9622 0.9622 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9576 0.9576 0.0 3 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.9540 0.9540 0.0 4 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.9308 0.9308 0.0 5 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.9215 0.9215 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8949 0.8949 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8657 0.8657 0.0 46 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.0000 0.8568 0.8568 0.0 111 -4.0000 0.0000 0.0000 -4.0000 0.0000 -4.0000 0.8473 0.8473 0.0 117 -4.0000 0.0000 0.0000 0.0000 -4.0000 -4.0000 0.8268 0.8268 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.7840 0.7840 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.7734 0.7734 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7421 0.7421 0.0 354 0.0000 0.0000 0.0000 -4.0000 0.0000 -4.0000 0.7047 0.7047 0.0 355 0.0000 0.0000 0.0000 -4.0000 0.0000 0.0000 0.5658 0.5658 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.3116 0.3116 0.0 Brute Force -------------------------- Min cost was 0.311583 Number of iterations 729 Search time 1.617000 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 -0.071 0.000 0.000 0.000 0.000 0.000 0.3091508141 10 -0.085 0.000 0.000 0.000 0.000 0.000 0.3089316637 11 -0.088 0.000 0.000 0.000 0.000 0.000 0.3089306297 13 -0.087 0.000 0.000 0.000 0.000 0.000 0.3089290344 14 -0.086 0.000 0.000 0.000 0.000 0.000 0.3089289007 16 -0.086 1.000 0.000 0.000 0.000 0.000 0.3053513078 20 -0.086 0.618 0.000 0.000 0.000 0.000 0.2939906912 21 -0.086 0.554 0.000 0.000 0.000 0.000 0.2907241836 22 -0.086 0.342 0.000 0.000 0.000 0.000 0.2892137256 23 -0.086 0.425 0.000 0.000 0.000 0.000 0.2855514415 24 -0.086 0.439 0.000 0.000 0.000 0.000 0.2853602182 26 -0.086 0.445 0.000 0.000 0.000 0.000 0.2853419820 30 -0.086 0.445 1.000 0.000 0.000 0.000 0.2756816100 34 -0.086 0.445 0.618 0.000 0.000 0.000 0.2679578337 37 -0.086 0.445 0.616 0.000 0.000 0.000 0.2679524226 38 -0.086 0.445 0.612 0.000 0.000 0.000 0.2679510357 40 -0.086 0.445 0.614 0.000 0.000 0.000 0.2679487636 44 -0.086 0.445 0.614 -1.618 0.000 0.000 0.2078583969 45 -0.086 0.445 0.614 -1.297 0.000 0.000 0.1945119891 48 -0.086 0.445 0.614 -1.108 0.000 0.000 0.1883502408 49 -0.086 0.445 0.614 -1.074 0.000 0.000 0.1877724148 51 -0.086 0.445 0.614 -1.035 0.000 0.000 0.1872842160 52 -0.086 0.445 0.614 -1.030 0.000 0.000 0.1872623722 53 -0.086 0.445 0.614 -1.022 0.000 0.000 0.1872466007 54 -0.086 0.445 0.614 -1.020 0.000 0.000 0.1872464578 64 -0.086 0.445 0.614 -1.020 0.041 0.000 0.1872098794 65 -0.086 0.445 0.614 -1.020 0.025 0.000 0.1871496326 66 -0.086 0.445 0.614 -1.020 0.023 0.000 0.1871468708 67 -0.086 0.445 0.614 -1.020 0.019 0.000 0.1871423925 69 -0.086 0.445 0.614 -1.020 0.017 0.000 0.1871414031 79 -0.086 0.445 0.614 -1.020 0.017 0.036 0.1867480779 81 -0.086 0.445 0.614 -1.020 0.017 0.035 0.1867462376 82 -0.086 0.445 0.614 -1.020 0.017 0.032 0.1867462116 85 -0.086 0.445 0.614 -1.020 0.017 0.033 0.1867457250 powell nthiter 1 96 -0.078 0.445 0.614 -1.020 0.017 0.033 0.1866909445 106 -0.078 0.505 0.614 -1.020 0.017 0.033 0.1862647398 107 -0.078 0.492 0.614 -1.020 0.017 0.033 0.1862085549 108 -0.078 0.489 0.614 -1.020 0.017 0.033 0.1862047173 109 -0.078 0.487 0.614 -1.020 0.017 0.033 0.1862031300 111 -0.078 0.486 0.614 -1.020 0.017 0.033 0.1862030009 119 -0.078 0.486 0.784 -1.020 0.017 0.033 0.1819760411 120 -0.078 0.486 0.791 -1.020 0.017 0.033 0.1819271995 122 -0.078 0.486 0.805 -1.020 0.017 0.033 0.1818652626 124 -0.078 0.486 0.806 -1.020 0.017 0.033 0.1818651711 132 -0.078 0.486 0.806 -1.123 0.017 0.033 0.1781938006 134 -0.078 0.486 0.806 -1.153 0.017 0.033 0.1781048646 135 -0.078 0.486 0.806 -1.144 0.017 0.033 0.1780425205 136 -0.078 0.486 0.806 -1.141 0.017 0.033 0.1780339401 137 -0.078 0.486 0.806 -1.139 0.017 0.033 0.1780336877 145 -0.078 0.486 0.806 -1.139 0.025 0.033 0.1779821088 146 -0.078 0.486 0.806 -1.139 0.046 0.033 0.1779154964 148 -0.078 0.486 0.806 -1.139 0.044 0.033 0.1779150025 150 -0.078 0.486 0.806 -1.139 0.045 0.033 0.1779148906 157 -0.078 0.486 0.806 -1.139 0.045 0.069 0.1778049251 158 -0.078 0.486 0.806 -1.139 0.045 0.076 0.1777683092 160 -0.078 0.486 0.806 -1.139 0.045 0.125 0.1774629380 162 -0.078 0.486 0.806 -1.139 0.045 0.116 0.1774128827 164 -0.078 0.486 0.806 -1.139 0.045 0.114 0.1774091665 powell nthiter 2 174 -0.121 0.486 0.806 -1.139 0.045 0.114 0.1772122669 175 -0.119 0.486 0.806 -1.139 0.045 0.114 0.1772099577 177 -0.120 0.486 0.806 -1.139 0.045 0.114 0.1772096874 189 -0.120 0.485 0.806 -1.139 0.045 0.114 0.1772089640 199 -0.120 0.485 0.812 -1.139 0.045 0.114 0.1771960601 201 -0.120 0.485 0.813 -1.139 0.045 0.114 0.1771960214 212 -0.120 0.485 0.813 -1.134 0.045 0.114 0.1771890758 213 -0.120 0.485 0.813 -1.135 0.045 0.114 0.1771887648 223 -0.120 0.485 0.813 -1.135 0.047 0.114 0.1771806189 224 -0.120 0.485 0.813 -1.135 0.051 0.114 0.1771789689 226 -0.120 0.485 0.813 -1.135 0.050 0.114 0.1771778564 235 -0.120 0.485 0.813 -1.135 0.050 0.174 0.1770022312 237 -0.120 0.485 0.813 -1.135 0.050 0.155 0.1767898461 239 -0.120 0.485 0.813 -1.135 0.050 0.156 0.1767882015 powell nthiter 3 251 -0.114 0.485 0.813 -1.135 0.050 0.156 0.1767448541 264 -0.114 0.481 0.813 -1.135 0.050 0.156 0.1767220265 266 -0.114 0.479 0.813 -1.135 0.050 0.156 0.1767199192 276 -0.114 0.479 0.815 -1.135 0.050 0.156 0.1767174343 285 -0.114 0.479 0.815 -1.152 0.050 0.156 0.1766299380 287 -0.114 0.479 0.815 -1.151 0.050 0.156 0.1766279014 288 -0.114 0.479 0.815 -1.149 0.050 0.156 0.1766261266 297 -0.114 0.479 0.815 -1.149 0.032 0.156 0.1765540494 299 -0.114 0.479 0.815 -1.149 0.036 0.156 0.1765454660 300 -0.114 0.479 0.815 -1.149 0.037 0.156 0.1765446344 310 -0.114 0.479 0.815 -1.149 0.037 0.151 0.1765362926 311 -0.114 0.479 0.815 -1.149 0.037 0.152 0.1765357610 powell nthiter 4 323 -0.109 0.479 0.815 -1.149 0.037 0.152 0.1765274019 324 -0.110 0.479 0.815 -1.149 0.037 0.152 0.1765255037 337 -0.110 0.482 0.815 -1.149 0.037 0.152 0.1765210375 356 -0.110 0.482 0.815 -1.157 0.037 0.152 0.1765169150 357 -0.110 0.482 0.815 -1.156 0.037 0.152 0.1765142874 358 -0.110 0.482 0.815 -1.153 0.037 0.152 0.1765125245 360 -0.110 0.482 0.815 -1.154 0.037 0.152 0.1765124893 367 -0.110 0.482 0.815 -1.154 0.026 0.152 0.1765095014 368 -0.110 0.482 0.815 -1.154 0.030 0.152 0.1765009655 369 -0.110 0.482 0.815 -1.154 0.031 0.152 0.1765004862 380 -0.110 0.482 0.815 -1.154 0.031 0.150 0.1764985912 powell nthiter 5 393 -0.109 0.482 0.815 -1.154 0.031 0.150 0.1764980196 417 -0.109 0.482 0.816 -1.154 0.031 0.150 0.1764976541 428 -0.109 0.482 0.816 -1.155 0.031 0.150 0.1764973010 438 -0.109 0.482 0.816 -1.155 0.030 0.150 0.1764968907 449 -0.109 0.482 0.816 -1.155 0.030 0.149 0.1764967636 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 1.013736 1 -25.0 -25.0 25.0 1.001880 2 -25.0 25.0 -25.0 1.009852 3 -25.0 25.0 25.0 0.986873 4 25.0 -25.0 -25.0 0.997113 5 25.0 -25.0 25.0 1.025638 6 25.0 25.0 -25.0 0.988435 7 25.0 25.0 25.0 1.058667 REL: 8 0.176497 8.082194 1.010274 rel = 0.174702 Number of iterations 5 Min cost was 0.176497 Number of FunctionCalls 451 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.808000 sec Parameters at optimum (transmm) -0.10933 0.48153 0.81627 Parameters at optimum (rotdeg) -1.15546 0.02989 0.14910 Final costs ---------------- Number of surface hits 2735 WM Intensity 234.1034 +/- 63.7311 Ctx Intensity 316.6350 +/- 88.0054 Pct Contrast 29.1835 +/- 23.6732 Cost 0.1765 RelCost 0.3087 Reg at min cost was 0.999 0.039 0.008 -0.159; 0.007 -0.385 0.923 -31.859; 0.039 -0.922 -0.385 3.473; 0.000 0.000 0.000 1.000; Writing optimal reg to /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/bbr.pass1.dat, type = 14 Original Reg 0.999 0.038 0.011 -0.135; 0.004 -0.367 0.930 -32.387; 0.040 -0.930 -0.367 2.004; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.003 0.024; -0.003 0.019 0.008 -0.528; 0.001 -0.008 0.019 -1.469; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 1.317425 Computing change in rh position Surface RMS Diff (mm) 1.334809 2.565733 mri_segreg done mri_segreg --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/bbr.pass1.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii --init-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/bbr.pass1.dat --out-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat.mincost --dof 6 --nmax 36 --param /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat.param --surf white --cur-reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/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-2012-12-18/dmri/xfms/tmp.bbregister.14312/template.nii regfile /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/tmp.bbregister.14312/bbr.pass1.dat subject nick-2012-12-18 dof 6 outregfile /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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 1367695150 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 0.008 -0.159; 0.007 -0.385 0.923 -31.859; 0.039 -0.922 -0.385 3.473; 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 1.013427 1 -25.0 -25.0 25.0 1.011518 2 -25.0 25.0 -25.0 1.010353 3 -25.0 25.0 25.0 0.996435 4 25.0 -25.0 -25.0 1.006443 5 25.0 -25.0 25.0 1.018685 6 25.0 25.0 -25.0 0.998803 7 25.0 25.0 25.0 1.003406 REL: 8 0.180800 8.059069 1.007384 rel = 0.179475 Initial costs ---------------- Number of surface hits 271549 WM Intensity 233.3160 +/- 64.9389 Ctx Intensity 315.2570 +/- 84.0800 Pct Contrast 29.2293 +/- 23.8122 Cost 0.1808 RelCost 0.1795 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1855 0.1855 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1848 0.1848 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1839 0.1839 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1820 0.1820 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.1802 0.1802 0.0 30 -0.1000 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1800 0.1800 0.0 33 -0.1000 -0.1000 0.0000 -0.1000 0.1000 -0.1000 0.1797 0.1797 0.0 112 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.0000 0.1795 0.1795 0.0 123 -0.1000 0.0000 0.0000 0.0000 0.1000 -0.1000 0.1780 0.1780 0.0 274 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1777 0.1777 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1777 0.1777 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1765 0.1765 0.0 Brute Force -------------------------- Min cost was 0.176497 Number of iterations 729 Search time 1.680000 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 0.000000 linmin_xtol_ 0.001000 powell nthiter 0 7 0.064 0.000 0.000 0.000 0.000 0.000 0.1805809895 10 0.068 0.000 0.000 0.000 0.000 0.000 0.1805792248 11 0.069 0.000 0.000 0.000 0.000 0.000 0.1805791202 19 0.069 -0.158 0.000 0.000 0.000 0.000 0.1784988092 20 0.069 -0.155 0.000 0.000 0.000 0.000 0.1784976359 30 0.069 -0.155 -0.004 0.000 0.000 0.000 0.1784974117 31 0.069 -0.155 -0.002 0.000 0.000 0.000 0.1784971982 39 0.069 -0.155 -0.002 -0.050 0.000 0.000 0.1782597576 41 0.069 -0.155 -0.002 -0.051 0.000 0.000 0.1782596857 49 0.069 -0.155 -0.002 -0.051 -0.047 0.000 0.1781793369 51 0.069 -0.155 -0.002 -0.051 -0.042 0.000 0.1781782288 52 0.069 -0.155 -0.002 -0.051 -0.043 0.000 0.1781782107 60 0.069 -0.155 -0.002 -0.051 -0.043 -0.095 0.1779820839 61 0.069 -0.155 -0.002 -0.051 -0.043 -0.067 0.1779357313 62 0.069 -0.155 -0.002 -0.051 -0.043 -0.066 0.1779356094 powell nthiter 1 72 0.067 -0.155 -0.002 -0.051 -0.043 -0.065 0.1779325109 73 0.060 -0.155 -0.002 -0.051 -0.043 -0.065 0.1779281056 75 0.059 -0.155 -0.002 -0.051 -0.043 -0.065 0.1779280319 83 0.059 -0.166 -0.002 -0.051 -0.043 -0.065 0.1779176135 93 0.059 -0.166 0.007 -0.051 -0.043 -0.065 0.1779153434 94 0.059 -0.166 0.005 -0.051 -0.043 -0.065 0.1779148942 95 0.059 -0.166 0.004 -0.051 -0.043 -0.065 0.1779148268 96 0.059 -0.166 0.003 -0.051 -0.043 -0.065 0.1779148239 105 0.059 -0.166 0.003 -0.045 -0.043 -0.065 0.1779123783 115 0.059 -0.166 0.003 -0.045 -0.042 -0.065 0.1779111942 116 0.059 -0.166 0.003 -0.045 -0.035 -0.065 0.1779039583 121 0.059 -0.166 0.003 -0.045 -0.032 -0.065 0.1779027669 132 0.059 -0.166 0.003 -0.045 -0.032 -0.066 0.1779026717 powell nthiter 2 142 0.053 -0.166 0.003 -0.045 -0.032 -0.066 0.1779010263 143 0.055 -0.166 0.003 -0.045 -0.032 -0.066 0.1779005656 151 0.055 -0.163 0.003 -0.045 -0.032 -0.066 0.1778992699 152 0.055 -0.162 0.003 -0.045 -0.032 -0.066 0.1778991549 161 0.055 -0.162 0.012 -0.045 -0.032 -0.066 0.1778963497 162 0.055 -0.162 0.011 -0.045 -0.032 -0.066 0.1778962328 171 0.055 -0.162 0.011 -0.042 -0.032 -0.066 0.1778952625 182 0.055 -0.162 0.011 -0.043 -0.028 -0.066 0.1778935461 192 0.055 -0.162 0.011 -0.043 -0.028 -0.071 0.1778931510 193 0.055 -0.162 0.011 -0.043 -0.028 -0.069 0.1778930097 powell nthiter 3 203 0.049 -0.162 0.011 -0.043 -0.028 -0.069 0.1778927878 204 0.052 -0.162 0.011 -0.043 -0.028 -0.069 0.1778918908 222 0.052 -0.162 0.014 -0.043 -0.028 -0.069 0.1778918205 223 0.052 -0.162 0.013 -0.043 -0.028 -0.069 0.1778918103 224 0.052 -0.162 0.012 -0.043 -0.028 -0.069 0.1778917536 232 0.052 -0.162 0.012 -0.041 -0.028 -0.069 0.1778913772 250 0.052 -0.162 0.012 -0.041 -0.028 -0.073 0.1778911949 253 0.049 -0.162 0.013 -0.040 -0.028 -0.074 0.1778911942 259 0.050 -0.162 0.012 -0.040 -0.028 -0.073 0.1778910086 261 0.050 -0.162 0.012 -0.041 -0.028 -0.073 0.1778909257 265 0.050 -0.162 0.012 -0.041 -0.028 -0.073 0.1778908707 powell nthiter 4 286 0.050 -0.161 0.012 -0.041 -0.028 -0.073 0.1778905914 287 0.050 -0.160 0.012 -0.041 -0.028 -0.073 0.1778905628 297 0.050 -0.160 0.015 -0.041 -0.028 -0.073 0.1778905211 299 0.050 -0.160 0.014 -0.041 -0.028 -0.073 0.1778904886 307 0.050 -0.160 0.014 -0.040 -0.028 -0.073 0.1778903978 327 0.050 -0.160 0.014 -0.040 -0.028 -0.073 0.1778903853 330 0.050 -0.160 0.014 -0.040 -0.028 -0.073 0.1778903698 powell nthiter 5 343 0.050 -0.160 0.014 -0.040 -0.028 -0.074 0.1778902708 385 0.049 -0.160 0.014 -0.039 -0.028 -0.075 0.1778902584 387 0.050 -0.160 0.014 -0.039 -0.028 -0.075 0.1778902019 powell nthiter 6 442 0.049 -0.160 0.014 -0.039 -0.028 -0.075 0.1778901876 powell nthiter 7 Powell done niters = 7 Computing relative cost 0 -25.0 -25.0 -25.0 1.012656 1 -25.0 -25.0 25.0 1.010949 2 -25.0 25.0 -25.0 1.010052 3 -25.0 25.0 25.0 0.995599 4 25.0 -25.0 -25.0 1.005095 5 25.0 -25.0 25.0 1.018558 6 25.0 25.0 -25.0 0.999295 7 25.0 25.0 25.0 1.005249 REL: 8 0.177890 8.057452 1.007182 rel = 0.176622 Number of iterations 7 Min cost was 0.177890 Number of FunctionCalls 515 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 77.598000 sec Parameters at optimum (transmm) 0.04907 -0.15957 0.01401 Parameters at optimum (rotdeg) -0.03893 -0.02795 -0.07505 Final costs ---------------- Number of surface hits 271549 WM Intensity 233.1620 +/- 65.3746 Ctx Intensity 314.7066 +/- 84.4015 Pct Contrast 29.1471 +/- 23.7305 Cost 0.1779 RelCost 0.1795 Reg at min cost was 0.999 0.039 0.010 -0.153; 0.006 -0.386 0.923 -32.016; 0.039 -0.922 -0.386 3.508; 0.000 0.000 0.000 1.000; Writing optimal reg to /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat, type = 14 Original Reg 0.999 0.039 0.008 -0.159; 0.007 -0.385 0.923 -31.859; 0.039 -0.922 -0.385 3.473; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.000 -0.001 -0.006; 0.001 0.001 0.000 0.157; -0.000 -0.000 0.001 -0.036; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.128485 Computing change in rh position Surface RMS Diff (mm) 0.163953 0.265853 mri_segreg done tkregister2_cmdl --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat --noedit --fslregout /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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-2012-12-18/dmri/dwi.nii.gz reg file /homes/10/ayendiki/tract/nicks/nick-2012-12-18/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 0.039 0.010 -0.153; 0.006 -0.386 0.923 -32.016; 0.039 -0.922 -0.386 3.508; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/terrier_002/users/nicks/subjects/nicks_recons/nick-2012-12-18/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-2012-12-18/dmri/dwi.nii.gz Tmov: -------------------- -2.000 0.000 0.000 128.000; 0.000 0.000 2.000 -64.000; 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 0.039 0.010 -0.153; 0.006 -0.386 0.923 -32.016; 0.039 -0.922 -0.386 3.508; 0.000 0.000 0.000 1.000; Determinant 1 subject = nick-2012-12-18 RegMat --------------------------- 0.999 0.039 0.010 -0.153; 0.006 -0.386 0.923 -32.016; 0.039 -0.922 -0.386 3.508; 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 21:24:18 EDT 2013 Ended at Wed Apr 24 21:28:36 EDT 2013 BBR-Run-Time-Sec 258 bbregister Done To check results, run: tkregister2 --mov /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/dwi.nii.gz --reg /homes/10/ayendiki/tract/nicks/nick-2012-12-18/dmri/xfms/anatorig2diff.bbr.dat --surf