Logfile for bbregister Mon Mar 28 17:55:16 EDT 2011 setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects cd /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 /space/crash/1/users/greve/freesurferx86/bin/bbregister --s fsf01anat --init-fsl --6 --bold --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --init-reg-out bold/001/init.register.dof6.dat $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux tanha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /space/crash/1/users/greve/freesurferx86 mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.19504/template.nii mri_convert bold/001/template.nii.gz bold/001/tmp.bbregister.19504/template.nii $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/001/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) writing to bold/001/tmp.bbregister.19504/template.nii... fslregister --s fsf01anat --mov bold/001/tmp.bbregister.19504/template.nii --reg bold/001/tmp.bbregister.19504/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.19504/fslregister --dof 6 Log file is bold/001/tmp.bbregister.19504/reg.init.dat.fslregister.log Mon Mar 28 17:55:16 EDT 2011 --s fsf01anat --mov bold/001/tmp.bbregister.19504/template.nii --reg bold/001/tmp.bbregister.19504/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/001/tmp.bbregister.19504/fslregister --dof 6 $Id: fslregister,v 1.35 2011/03/28 20:35:14 greve Exp $ tanha Linux tanha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_convert /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/mri/brainmask.mgz bold/001/tmp.bbregister.19504/fslregister/refvol.fslregister.nii mri_convert /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/mri/brainmask.mgz bold/001/tmp.bbregister.19504/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.60053e-09, 3.87945e-08) j_ras = (1.95259e-16, -2.98023e-08, -1) k_ras = (1.49012e-08, 1, 2.98023e-08) writing to bold/001/tmp.bbregister.19504/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_convert bold/001/tmp.bbregister.19504/template.nii bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/001/tmp.bbregister.19504/template.nii bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/001/tmp.bbregister.19504/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -0.973976, -0.226651) k_ras = (-2.36491e-18, -0.226651, 0.973976) keeping frame 0 writing to bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii... Mov determinant is 59.082 Swapping dims for pos det WARNING:: Flipping Left/Right orientation (as det < 0) tkregister_tcl /space/crash/1/users/greve/freesurferx86/tktools/tkregister2.tcl target volume bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii movable volume bold/001/tmp.bbregister.19504/template.nii reg file bold/001/tmp.bbregister.19504/fslregister/swapreg.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.122 2011/03/28 20:24:46 greve Exp $ Diagnostic Level -1 INFO: loading target bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. 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 bold/001/tmp.bbregister.19504/template.nii Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 5.000 -75.000; 0.000 -3.437 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.000 -0.000 0.000 3.437; 0.000 -0.227 0.974 0.000; 0.000 0.974 0.227 0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 1.000 -0.000 0.000 3.437; 0.000 -0.227 0.974 0.000; 0.000 0.974 0.227 0.000; 0.000 0.000 0.000 1.000; Determinant -1 subject = subject-unknown RegMat --------------------------- -1.000 0.000 -0.000 3.437; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 tkregister2_cmdl --mov bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii --reg bold/001/tmp.bbregister.19504/fslregister/reg0.19538.dat --regheader --fslregout bold/001/tmp.bbregister.19504/reg.init.dat.fsl.mat0 --s fsf01anat --noedit tkregister_tcl /space/crash/1/users/greve/freesurferx86/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii reg file bold/001/tmp.bbregister.19504/fslregister/reg0.19538.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.122 2011/03/28 20:24:46 greve Exp $ Diagnostic Level -1 INFO: loading target /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/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 bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 5.000 -75.000; 0.000 -3.437 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -1.000 -0.000 0.000 -3.804; -0.000 -0.227 0.974 -90.534; -0.000 0.974 0.227 28.213; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 -0.000 0.000 -3.804; -0.000 -0.227 0.974 -90.534; -0.000 0.974 0.227 28.213; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsf01anat RegMat --------------------------- -1.000 -0.000 0.000 -3.804; -0.000 -0.227 0.974 -90.534; -0.000 0.974 0.227 28.213; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -59.082, ref det = -1 Mon Mar 28 17:55:19 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/001/tmp.bbregister.19504/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.19504/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/4.1.4/etc/flirtsch/xyztrans.sch -init bold/001/tmp.bbregister.19504/reg.init.dat.fsl.mat0 Mon Mar 28 17:55:28 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/001/tmp.bbregister.19504/fslregister/refvol.fslregister.nii -in bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/001/tmp.bbregister.19504/reg.init.dat.fsl.mat -init bold/001/tmp.bbregister.19504/fslregister/fslmat0.trans.mat -schedule /space/crash/1/users/greve/freesurferx86/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s fsf01anat --mov bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii --reg bold/001/tmp.bbregister.19504/reg.init.dat --fslreg bold/001/tmp.bbregister.19504/reg.init.dat.fsl.mat --noedit tkregister_tcl /space/crash/1/users/greve/freesurferx86/tktools/tkregister2.tcl ---- FSL registration matrix -------- -1.000 -0.000 -0.000 234.956; -0.000 0.249 -0.968 138.073; -0.000 -0.968 -0.249 245.602; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii reg file bold/001/tmp.bbregister.19504/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.122 2011/03/28 20:24:46 greve Exp $ Diagnostic Level -1 INFO: loading target /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/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 bold/001/tmp.bbregister.19504/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.438 0.000 0.000 110.000; 0.000 0.000 5.000 -75.000; 0.000 -3.437 0.000 110.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -59.082, ref det = -1 ---- Input registration matrix (computed) -------- -1.000 -0.000 -0.000 3.044; -0.000 -0.249 0.968 -35.953; 0.000 0.968 0.249 -1.387; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 -0.000 -0.000 3.044; -0.000 -0.249 0.968 -35.953; 0.000 0.968 0.249 -1.387; 0.000 0.000 0.000 1.000; Determinant 0.999999 subject = fsf01anat RegMat --------------------------- -1.000 -0.000 -0.000 3.044; -0.000 -0.249 0.968 -35.953; 0.000 0.968 0.249 -1.387; 0.000 0.000 0.000 1.000; mri_matrix_multiply -im bold/001/tmp.bbregister.19504/fslregister/swapreg.dat -im bold/001/tmp.bbregister.19504/reg.init.dat -om bold/001/tmp.bbregister.19504/reg.init.dat Started at Mon Mar 28 17:55:16 EDT 2011 Ended at Mon Mar 28 17:55:47 EDT 2011 fslregister Done To check results, run: tkregister2 --mov bold/001/tmp.bbregister.19504/template.nii --reg bold/001/tmp.bbregister.19504/reg.init.dat --surf orig mri_segreg --mov bold/001/tmp.bbregister.19504/template.nii --init-reg bold/001/tmp.bbregister.19504/reg.init.dat --out-reg bold/001/tmp.bbregister.19504/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects cd /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_segreg --mov bold/001/tmp.bbregister.19504/template.nii --init-reg bold/001/tmp.bbregister.19504/reg.init.dat --out-reg bold/001/tmp.bbregister.19504/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 tanha machine x86_64 user greve movvol bold/001/tmp.bbregister.19504/template.nii regfile bold/001/tmp.bbregister.19504/reg.init.dat subject fsf01anat dof 6 outregfile bold/001/tmp.bbregister.19504/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 1301599024 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 0.000 0.000 0.393; -0.000 -0.249 0.968 -35.953; 0.000 0.968 0.249 -1.387; 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 1.082329 1 -25.0 -25.0 25.0 1.040167 2 -25.0 25.0 -25.0 1.066219 3 -25.0 25.0 25.0 1.075697 4 25.0 -25.0 -25.0 1.090109 5 25.0 -25.0 25.0 1.034954 6 25.0 25.0 -25.0 1.037225 7 25.0 25.0 25.0 1.058078 REL: 8 0.910970 8.484778 1.060597 rel = 0.858921 Initial costs ---------------- Number of surface hits 3040 WM Intensity 874.2648 +/- 204.0333 Ctx Intensity 851.6286 +/- 238.1873 Pct Contrast -4.5796 +/- 23.8929 Cost 0.9110 RelCost 0.8589 WARNING: initial G-W contrast is negative, but expecting positive. If the mov data has a T1 contrast, re-run with --T1 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 1.0508 1.0508 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 1.0302 1.0302 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 1.0196 1.0196 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 1.0146 1.0146 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9808 0.9808 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9528 0.9528 0.0 16 -4.0000 -4.0000 -4.0000 0.0000 4.0000 0.0000 0.9461 0.9461 0.0 27 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.9394 0.9394 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.9096 0.9096 0.0 253 0.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9084 0.9084 0.0 255 0.0000 -4.0000 -4.0000 0.0000 0.0000 -4.0000 0.9070 0.9070 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8293 0.8293 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.7998 0.7998 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7241 0.7241 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6059 0.6059 0.0 Brute Force -------------------------- Min cost was 0.605928 Number of iterations 729 Search time 1.785000 sec Parameters at best (transmm, rotdeg) 0.000 -4.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -4 2 0 3 0 4 0 5 0 6 0.382 -4.000 0.000 0.000 0.000 0.000 0.6024303187 8 0.468 -4.000 0.000 0.000 0.000 0.000 0.6022677898 9 0.474 -4.000 0.000 0.000 0.000 0.000 0.6022529889 10 0.536 -4.000 0.000 0.000 0.000 0.000 0.6022417063 11 0.508 -4.000 0.000 0.000 0.000 0.000 0.6021987376 16 0.508 -5.618 0.000 0.000 0.000 0.000 0.5974991486 17 0.508 -4.901 0.000 0.000 0.000 0.000 0.5887797494 21 0.508 -4.841 0.000 0.000 0.000 0.000 0.5885265630 22 0.508 -4.802 0.000 0.000 0.000 0.000 0.5884542386 24 0.508 -4.800 0.000 0.000 0.000 0.000 0.5884535676 25 0.508 -4.799 0.000 0.000 0.000 0.000 0.5884533543 32 0.508 -4.799 -0.618 0.000 0.000 0.000 0.5847290420 34 0.508 -4.799 -0.439 0.000 0.000 0.000 0.5842995075 35 0.508 -4.799 -0.466 0.000 0.000 0.000 0.5841109928 36 0.508 -4.799 -0.509 0.000 0.000 0.000 0.5840117110 37 0.508 -4.799 -0.505 0.000 0.000 0.000 0.5840112115 38 0.508 -4.799 -0.506 0.000 0.000 0.000 0.5840111360 44 0.508 -4.799 -0.506 -0.618 0.000 0.000 0.5821080538 47 0.508 -4.799 -0.506 -0.668 0.000 0.000 0.5821074622 48 0.508 -4.799 -0.506 -0.643 0.000 0.000 0.5820853200 50 0.508 -4.799 -0.506 -0.648 0.000 0.000 0.5820846666 53 0.508 -4.799 -0.506 -0.651 0.000 0.000 0.5820845791 55 0.508 -4.799 -0.506 -0.650 0.000 0.000 0.5820843621 62 0.508 -4.799 -0.506 -0.650 0.011 0.000 0.5820785706 63 0.508 -4.799 -0.506 -0.650 0.015 0.000 0.5820784950 71 0.508 -4.799 -0.506 -0.650 0.013 0.382 0.5806555630 73 0.508 -4.799 -0.506 -0.650 0.013 0.291 0.5804716628 75 0.508 -4.799 -0.506 -0.650 0.013 0.313 0.5804652120 77 0.508 -4.799 -0.506 -0.650 0.013 0.304 0.5804608514 91 0.491 -4.799 -0.506 -0.650 0.013 0.304 0.5804149271 92 0.487 -4.799 -0.506 -0.650 0.013 0.304 0.5804120748 93 0.485 -4.799 -0.506 -0.650 0.013 0.304 0.5804115096 100 0.485 -4.417 -0.506 -0.650 0.013 0.304 0.5762151325 103 0.485 -4.370 -0.506 -0.650 0.013 0.304 0.5760579870 104 0.485 -4.360 -0.506 -0.650 0.013 0.304 0.5760451323 105 0.485 -4.350 -0.506 -0.650 0.013 0.304 0.5760398863 106 0.485 -4.347 -0.506 -0.650 0.013 0.304 0.5760396980 114 0.485 -4.347 -0.124 -0.650 0.013 0.304 0.5755606921 115 0.485 -4.347 -0.288 -0.650 0.013 0.304 0.5742746105 116 0.485 -4.347 -0.300 -0.650 0.013 0.304 0.5742734409 117 0.485 -4.347 -0.295 -0.650 0.013 0.304 0.5742733833 118 0.485 -4.347 -0.297 -0.650 0.013 0.304 0.5742730657 119 0.485 -4.347 -0.298 -0.650 0.013 0.304 0.5742730599 128 0.485 -4.347 -0.298 -0.662 0.013 0.304 0.5742661969 130 0.485 -4.347 -0.298 -0.663 0.013 0.304 0.5742661950 138 0.485 -4.347 -0.298 -0.663 0.090 0.304 0.5735868362 139 0.485 -4.347 -0.298 -0.663 0.125 0.304 0.5733586020 141 0.485 -4.347 -0.298 -0.663 0.155 0.304 0.5732422812 143 0.485 -4.347 -0.298 -0.663 0.163 0.304 0.5732288802 144 0.485 -4.347 -0.298 -0.663 0.166 0.304 0.5732279693 146 0.485 -4.347 -0.298 -0.663 0.165 0.304 0.5732276073 153 0.485 -4.347 -0.298 -0.663 0.165 0.185 0.5729125745 154 0.485 -4.347 -0.298 -0.663 0.165 0.198 0.5729097619 155 0.485 -4.347 -0.298 -0.663 0.165 0.195 0.5729094712 165 0.330 -4.347 -0.298 -0.663 0.165 0.195 0.5726895417 166 0.389 -4.347 -0.298 -0.663 0.165 0.195 0.5724480506 167 0.395 -4.347 -0.298 -0.663 0.165 0.195 0.5724426755 168 0.401 -4.347 -0.298 -0.663 0.165 0.195 0.5724347896 171 0.407 -4.347 -0.298 -0.663 0.165 0.195 0.5724316237 173 0.406 -4.347 -0.298 -0.663 0.165 0.195 0.5724310785 182 0.406 -4.352 -0.298 -0.663 0.165 0.195 0.5724251157 183 0.406 -4.360 -0.298 -0.663 0.165 0.195 0.5724198773 185 0.406 -4.362 -0.298 -0.663 0.165 0.195 0.5724196432 186 0.406 -4.361 -0.298 -0.663 0.165 0.195 0.5724196031 195 0.406 -4.361 -0.286 -0.663 0.165 0.195 0.5724085114 196 0.406 -4.361 -0.288 -0.663 0.165 0.195 0.5724075914 197 0.406 -4.361 -0.289 -0.663 0.165 0.195 0.5724074890 208 0.406 -4.361 -0.289 -0.654 0.165 0.195 0.5724067528 209 0.406 -4.361 -0.289 -0.658 0.165 0.195 0.5724059383 219 0.406 -4.361 -0.289 -0.658 0.134 0.195 0.5720594763 220 0.406 -4.361 -0.289 -0.658 0.113 0.195 0.5719928136 230 0.406 -4.361 -0.289 -0.658 0.113 0.182 0.5719770026 231 0.406 -4.361 -0.289 -0.658 0.113 0.178 0.5719758884 243 0.393 -4.361 -0.289 -0.658 0.113 0.178 0.5719522998 245 0.395 -4.361 -0.289 -0.658 0.113 0.178 0.5719514571 246 0.396 -4.361 -0.289 -0.658 0.113 0.178 0.5719513351 256 0.396 -4.374 -0.289 -0.658 0.113 0.178 0.5719376183 268 0.396 -4.374 -0.275 -0.658 0.113 0.178 0.5718925465 269 0.396 -4.374 -0.269 -0.658 0.113 0.178 0.5718898919 280 0.396 -4.374 -0.270 -0.664 0.113 0.178 0.5718878122 281 0.396 -4.374 -0.270 -0.663 0.113 0.178 0.5718870719 292 0.396 -4.374 -0.270 -0.663 0.110 0.178 0.5718866956 294 0.396 -4.374 -0.270 -0.663 0.111 0.178 0.5718864341 306 0.396 -4.374 -0.270 -0.663 0.111 0.177 0.5718857760 328 0.396 -4.379 -0.270 -0.663 0.111 0.177 0.5718844114 340 0.396 -4.379 -0.271 -0.663 0.111 0.177 0.5718843055 350 0.396 -4.379 -0.271 -0.668 0.111 0.177 0.5718841706 351 0.396 -4.379 -0.271 -0.665 0.111 0.177 0.5718837672 376 0.396 -4.379 -0.271 -0.665 0.111 0.176 0.5718837163 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.046637 1 -25.0 -25.0 25.0 1.059162 2 -25.0 25.0 -25.0 1.058404 3 -25.0 25.0 25.0 1.068588 4 25.0 -25.0 -25.0 1.050676 5 25.0 -25.0 25.0 1.058278 6 25.0 25.0 -25.0 1.008659 7 25.0 25.0 25.0 1.039727 REL: 8 0.571884 8.390131 1.048766 rel = 0.545292 Number of iterations 4 Min cost was 0.571884 Number of FunctionCalls 378 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.926000 sec Parameters at optimum (transmm) 0.39603 -4.37870 -0.27148 Parameters at optimum (rotdeg) -0.66545 0.11126 0.17609 Final costs ---------------- Number of surface hits 3040 WM Intensity 823.1370 +/- 219.1023 Ctx Intensity 850.7216 +/- 251.0803 Pct Contrast 1.2968 +/- 21.2321 Cost 0.5719 RelCost 0.8589 Reg at min cost was 1.000 0.003 -0.003 0.898; 0.003 -0.238 0.971 -40.344; -0.002 0.971 0.238 -1.242; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/tmp.bbregister.19504/bbr.pass1.dat, type = 14 Original Reg 1.000 0.000 0.000 0.393; -0.000 -0.249 0.968 -35.953; 0.000 0.968 0.249 -1.387; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 -0.003 0.003 -0.505; -0.003 -0.011 -0.003 4.391; 0.002 -0.003 0.011 -0.145; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 4.571991 Computing change in rh position Surface RMS Diff (mm) 4.482249 5.556006 WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1 mri_segreg done mri_segreg --mov bold/001/tmp.bbregister.19504/template.nii --init-reg bold/001/tmp.bbregister.19504/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.19504/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.103 2011/03/02 00:04:24 nicks Exp $ setenv SUBJECTS_DIR /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects cd /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_segreg --mov bold/001/tmp.bbregister.19504/template.nii --init-reg bold/001/tmp.bbregister.19504/bbr.pass1.dat --out-reg bold/001/register.dof6.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/001/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/001/register.dof6.dat.param --surf white --cur-reg bold/001/tmp.bbregister.19504/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname tanha machine x86_64 user greve movvol bold/001/tmp.bbregister.19504/template.nii regfile bold/001/tmp.bbregister.19504/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/001/register.dof6.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 1301920186 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 0.003 -0.003 0.898; 0.003 -0.238 0.971 -40.344; -0.002 0.971 0.238 -1.242; 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 1.041958 1 -25.0 -25.0 25.0 1.059143 2 -25.0 25.0 -25.0 1.061923 3 -25.0 25.0 25.0 1.067531 4 25.0 -25.0 -25.0 1.044085 5 25.0 -25.0 25.0 1.037772 6 25.0 25.0 -25.0 1.029357 7 25.0 25.0 25.0 1.059860 REL: 8 0.575902 8.401629 1.050204 rel = 0.548372 Initial costs ---------------- Number of surface hits 304441 WM Intensity 824.4495 +/- 216.4859 Ctx Intensity 852.1878 +/- 248.1665 Pct Contrast 1.4851 +/- 21.7352 Cost 0.5759 RelCost 0.5484 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5758 0.5758 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5754 0.5754 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5750 0.5750 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5749 0.5749 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5741 0.5741 0.0 32 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.5738 0.5738 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5733 0.5733 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5730 0.5730 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5724 0.5724 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5719 0.5719 0.0 Brute Force -------------------------- Min cost was 0.571884 Number of iterations 729 Search time 1.766000 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 -0.183 0.000 0.000 0.000 0.000 0.000 0.5752402734 8 -0.173 0.000 0.000 0.000 0.000 0.000 0.5752355636 10 -0.171 0.000 0.000 0.000 0.000 0.000 0.5752354401 18 -0.171 -0.122 0.000 0.000 0.000 0.000 0.5749148113 19 -0.171 -0.121 0.000 0.000 0.000 0.000 0.5749147928 32 -0.171 -0.119 -0.064 0.000 0.000 0.000 0.5748060022 33 -0.171 -0.119 -0.065 0.000 0.000 0.000 0.5748058767 34 -0.171 -0.119 -0.066 0.000 0.000 0.000 0.5748058197 43 -0.171 -0.119 -0.066 0.066 0.000 0.000 0.5747261630 44 -0.171 -0.119 -0.066 0.065 0.000 0.000 0.5747259943 45 -0.171 -0.119 -0.066 0.061 0.000 0.000 0.5747255448 47 -0.171 -0.119 -0.066 0.059 0.000 0.000 0.5747254144 58 -0.171 -0.119 -0.066 0.059 -0.131 0.000 0.5742577588 59 -0.171 -0.119 -0.066 0.059 -0.128 0.000 0.5742577344 61 -0.171 -0.119 -0.066 0.059 -0.129 0.000 0.5742575615 69 -0.171 -0.119 -0.066 0.059 -0.129 -0.131 0.5740512529 71 -0.171 -0.119 -0.066 0.059 -0.129 -0.119 0.5740493533 73 -0.171 -0.119 -0.066 0.059 -0.129 -0.120 0.5740490841 74 -0.171 -0.119 -0.066 0.059 -0.129 -0.122 0.5740490526 84 -0.181 -0.119 -0.066 0.059 -0.129 -0.122 0.5740473648 94 -0.179 -0.143 -0.066 0.059 -0.129 -0.122 0.5740389707 96 -0.179 -0.139 -0.066 0.059 -0.129 -0.122 0.5740377934 97 -0.179 -0.137 -0.066 0.059 -0.129 -0.122 0.5740377808 99 -0.179 -0.138 -0.066 0.059 -0.129 -0.122 0.5740376206 106 -0.179 -0.138 -0.073 0.059 -0.129 -0.122 0.5740367649 107 -0.179 -0.138 -0.072 0.059 -0.129 -0.122 0.5740367394 115 -0.179 -0.138 -0.072 0.075 -0.129 -0.122 0.5740365450 116 -0.179 -0.138 -0.072 0.067 -0.129 -0.122 0.5740350620 125 -0.179 -0.138 -0.072 0.067 -0.148 -0.122 0.5740278413 126 -0.179 -0.138 -0.072 0.067 -0.145 -0.122 0.5740274273 136 -0.179 -0.138 -0.072 0.067 -0.144 -0.115 0.5740273158 138 -0.179 -0.138 -0.072 0.067 -0.144 -0.118 0.5740270745 150 -0.182 -0.138 -0.072 0.067 -0.144 -0.118 0.5740269685 161 -0.182 -0.140 -0.072 0.067 -0.144 -0.118 0.5740269430 163 -0.182 -0.139 -0.072 0.067 -0.144 -0.118 0.5740269166 172 -0.182 -0.139 -0.073 0.067 -0.144 -0.118 0.5740268979 181 -0.182 -0.139 -0.073 0.068 -0.144 -0.118 0.5740268912 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.042623 1 -25.0 -25.0 25.0 1.059110 2 -25.0 25.0 -25.0 1.061221 3 -25.0 25.0 25.0 1.067031 4 25.0 -25.0 -25.0 1.041187 5 25.0 -25.0 25.0 1.038377 6 25.0 25.0 -25.0 1.026332 7 25.0 25.0 25.0 1.058144 REL: 8 0.574027 8.394025 1.049253 rel = 0.547081 Number of iterations 3 Min cost was 0.574027 Number of FunctionCalls 267 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 41.372000 sec Parameters at optimum (transmm) -0.18267 -0.14026 -0.07328 Parameters at optimum (rotdeg) 0.06722 -0.14424 -0.11830 Final costs ---------------- Number of surface hits 304441 WM Intensity 822.8227 +/- 217.8419 Ctx Intensity 850.7266 +/- 249.7073 Pct Contrast 1.4814 +/- 21.8880 Cost 0.5740 RelCost 0.5484 Reg at min cost was 1.000 -0.000 -0.001 0.635; 0.001 -0.239 0.971 -40.485; 0.001 0.971 0.239 -1.360; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/001/register.dof6.dat, type = 14 Original Reg 1.000 0.003 -0.003 0.898; 0.003 -0.238 0.971 -40.344; -0.002 0.971 0.238 -1.242; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.003 -0.001 0.263; 0.002 0.001 0.000 0.141; -0.003 0.000 -0.001 0.118; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.270491 Computing change in rh position Surface RMS Diff (mm) 0.280346 0.565240 mri_segreg done Cleaning up Started at Mon Mar 28 17:55:16 EDT 2011 Ended at Mon Mar 28 17:57:00 EDT 2011 BBR-Run-Time-Sec 104 bbregister Done To check results, run: tkregister2 --mov bold/001/template.nii.gz --reg bold/001/register.dof6.dat --surf