Logfile for bbregister Mon Mar 28 17:58:41 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 --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --init-reg-out bold/002/init.register.dof6.dat --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --init-reg-out bold/003/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/003/template.nii.gz bold/003/tmp.bbregister.19926/template.nii mri_convert bold/003/template.nii.gz bold/003/tmp.bbregister.19926/template.nii $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/003/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/003/tmp.bbregister.19926/template.nii... fslregister --s fsf01anat --mov bold/003/tmp.bbregister.19926/template.nii --reg bold/003/tmp.bbregister.19926/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/003/tmp.bbregister.19926/fslregister --dof 6 Log file is bold/003/tmp.bbregister.19926/reg.init.dat.fslregister.log Mon Mar 28 17:58:41 EDT 2011 --s fsf01anat --mov bold/003/tmp.bbregister.19926/template.nii --reg bold/003/tmp.bbregister.19926/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/fslregister/refvol.fslregister.nii mri_convert /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/mri/brainmask.mgz bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_convert bold/003/tmp.bbregister.19926/template.nii bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/003/tmp.bbregister.19926/template.nii bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii movable volume bold/003/tmp.bbregister.19926/template.nii reg file bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii --reg bold/003/tmp.bbregister.19926/fslregister/reg0.19960.dat --regheader --fslregout bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii reg file bold/003/tmp.bbregister.19926/fslregister/reg0.19960.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/003/tmp.bbregister.19926/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 17:58:44 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/003/tmp.bbregister.19926/fslregister/refvol.fslregister.nii -in bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/003/tmp.bbregister.19926/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/4.1.4/etc/flirtsch/xyztrans.sch -init bold/003/tmp.bbregister.19926/reg.init.dat.fsl.mat0 Mon Mar 28 17:58:52 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/003/tmp.bbregister.19926/fslregister/refvol.fslregister.nii -in bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/003/tmp.bbregister.19926/reg.init.dat.fsl.mat -init bold/003/tmp.bbregister.19926/fslregister/fslmat0.trans.mat -schedule /space/crash/1/users/greve/freesurferx86/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s fsf01anat --mov bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii --reg bold/003/tmp.bbregister.19926/reg.init.dat --fslreg bold/003/tmp.bbregister.19926/reg.init.dat.fsl.mat --noedit tkregister_tcl /space/crash/1/users/greve/freesurferx86/tktools/tkregister2.tcl ---- FSL registration matrix -------- -1.000 0.007 0.020 232.286; -0.018 0.263 -0.965 137.486; -0.012 -0.965 -0.263 247.204; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/003/tmp.bbregister.19926/fslregister/movvol.fslregister.nii reg file bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/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 0.012 -0.018 4.178; -0.020 -0.263 0.965 -36.614; 0.007 0.965 0.263 -1.818; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 0.012 -0.018 4.178; -0.020 -0.263 0.965 -36.614; 0.007 0.965 0.263 -1.818; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsf01anat RegMat --------------------------- -1.000 0.012 -0.018 4.178; -0.020 -0.263 0.965 -36.614; 0.007 0.965 0.263 -1.818; 0.000 0.000 0.000 1.000; mri_matrix_multiply -im bold/003/tmp.bbregister.19926/fslregister/swapreg.dat -im bold/003/tmp.bbregister.19926/reg.init.dat -om bold/003/tmp.bbregister.19926/reg.init.dat Started at Mon Mar 28 17:58:41 EDT 2011 Ended at Mon Mar 28 17:59:10 EDT 2011 fslregister Done To check results, run: tkregister2 --mov bold/003/tmp.bbregister.19926/template.nii --reg bold/003/tmp.bbregister.19926/reg.init.dat --surf orig mri_segreg --mov bold/003/tmp.bbregister.19926/template.nii --init-reg bold/003/tmp.bbregister.19926/reg.init.dat --out-reg bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/template.nii --init-reg bold/003/tmp.bbregister.19926/reg.init.dat --out-reg bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/template.nii regfile bold/003/tmp.bbregister.19926/reg.init.dat subject fsf01anat dof 6 outregfile bold/003/tmp.bbregister.19926/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 1302309970 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.012 0.018 -0.741; -0.020 -0.263 0.965 -36.614; 0.007 0.965 0.263 -1.818; 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 1.074729 1 -25.0 -25.0 25.0 1.045396 2 -25.0 25.0 -25.0 1.072834 3 -25.0 25.0 25.0 1.073756 4 25.0 -25.0 -25.0 1.073346 5 25.0 -25.0 25.0 1.048601 6 25.0 25.0 -25.0 1.043739 7 25.0 25.0 25.0 1.069994 REL: 8 0.901581 8.502395 1.062799 rel = 0.848308 Initial costs ---------------- Number of surface hits 3040 WM Intensity 869.2234 +/- 199.6193 Ctx Intensity 847.6943 +/- 231.5310 Pct Contrast -4.4194 +/- 22.8304 Cost 0.9016 RelCost 0.8483 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 1.0250 1.0250 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9906 0.9906 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9807 0.9807 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9636 0.9636 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9433 0.9433 0.0 27 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.9317 0.9317 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8975 0.8975 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8775 0.8775 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8698 0.8698 0.0 273 0.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8598 0.8598 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7738 0.7738 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6144 0.6144 0.0 Brute Force -------------------------- Min cost was 0.614433 Number of iterations 729 Search time 1.789000 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 7 -0.262 -4.000 0.000 0.000 0.000 0.000 0.6144226664 8 -0.144 -4.000 0.000 0.000 0.000 0.000 0.6135484971 9 -0.131 -4.000 0.000 0.000 0.000 0.000 0.6135460991 10 -0.136 -4.000 0.000 0.000 0.000 0.000 0.6135429695 11 -0.137 -4.000 0.000 0.000 0.000 0.000 0.6135426487 12 -0.138 -4.000 0.000 0.000 0.000 0.000 0.6135424310 19 -0.138 -4.618 0.000 0.000 0.000 0.000 0.6045304340 23 -0.138 -4.572 0.000 0.000 0.000 0.000 0.6044350796 25 -0.138 -4.582 0.000 0.000 0.000 0.000 0.6044239859 27 -0.138 -4.583 0.000 0.000 0.000 0.000 0.6044238055 28 -0.138 -4.584 0.000 0.000 0.000 0.000 0.6044237405 36 -0.138 -4.585 -0.618 0.000 0.000 0.000 0.6035720718 38 -0.138 -4.585 -0.334 0.000 0.000 0.000 0.6034754070 39 -0.138 -4.585 -0.443 0.000 0.000 0.000 0.6028896060 40 -0.138 -4.585 -0.471 0.000 0.000 0.000 0.6027269553 41 -0.138 -4.585 -0.527 0.000 0.000 0.000 0.6026151169 42 -0.138 -4.585 -0.521 0.000 0.000 0.000 0.6025999111 43 -0.138 -4.585 -0.510 0.000 0.000 0.000 0.6025865286 46 -0.138 -4.585 -0.509 0.000 0.000 0.000 0.6025858826 55 -0.138 -4.585 -0.508 -0.294 0.000 0.000 0.6022450835 56 -0.138 -4.585 -0.508 -0.257 0.000 0.000 0.6017058918 58 -0.138 -4.585 -0.508 -0.219 0.000 0.000 0.6014183234 66 -0.138 -4.585 -0.508 -0.219 -0.618 0.000 0.5833816306 68 -0.138 -4.585 -0.508 -0.219 -0.645 0.000 0.5833620531 69 -0.138 -4.585 -0.508 -0.219 -0.640 0.000 0.5833607252 71 -0.138 -4.585 -0.508 -0.219 -0.641 0.000 0.5833607162 74 -0.138 -4.585 -0.508 -0.219 -0.641 1.000 0.5758815575 78 -0.138 -4.585 -0.508 -0.219 -0.641 0.618 0.5743807040 79 -0.138 -4.585 -0.508 -0.219 -0.641 0.532 0.5741818190 83 -0.138 -4.585 -0.508 -0.219 -0.641 0.534 0.5741807763 84 -0.138 -4.585 -0.508 -0.219 -0.641 0.535 0.5741798990 93 -0.248 -4.585 -0.508 -0.219 -0.641 0.535 0.5741124213 98 -0.276 -4.585 -0.508 -0.219 -0.641 0.535 0.5739452361 100 -0.280 -4.585 -0.508 -0.219 -0.641 0.535 0.5739399194 101 -0.281 -4.585 -0.508 -0.219 -0.641 0.535 0.5739390226 102 -0.283 -4.585 -0.508 -0.219 -0.641 0.535 0.5739388937 110 -0.283 -4.584 -0.508 -0.219 -0.641 0.535 0.5739312542 111 -0.283 -4.512 -0.508 -0.219 -0.641 0.535 0.5737396944 113 -0.283 -4.529 -0.508 -0.219 -0.641 0.535 0.5737107911 115 -0.283 -4.528 -0.508 -0.219 -0.641 0.535 0.5737107355 123 -0.283 -4.528 -0.384 -0.219 -0.641 0.535 0.5729595220 125 -0.283 -4.528 -0.403 -0.219 -0.641 0.535 0.5729216939 127 -0.283 -4.528 -0.413 -0.219 -0.641 0.535 0.5729102457 128 -0.283 -4.528 -0.424 -0.219 -0.641 0.535 0.5729085388 129 -0.283 -4.528 -0.420 -0.219 -0.641 0.535 0.5729068857 130 -0.283 -4.528 -0.419 -0.219 -0.641 0.535 0.5729068054 138 -0.283 -4.528 -0.419 -0.169 -0.641 0.535 0.5726775109 140 -0.283 -4.528 -0.419 -0.164 -0.641 0.535 0.5726766989 141 -0.283 -4.528 -0.419 -0.166 -0.641 0.535 0.5726766642 149 -0.283 -4.528 -0.419 -0.166 -0.636 0.535 0.5726230156 150 -0.283 -4.528 -0.419 -0.166 -0.566 0.535 0.5725489153 152 -0.283 -4.528 -0.419 -0.166 -0.597 0.535 0.5724275154 153 -0.283 -4.528 -0.419 -0.166 -0.598 0.535 0.5724266627 165 -0.283 -4.528 -0.419 -0.166 -0.598 0.543 0.5724099072 167 -0.283 -4.528 -0.419 -0.166 -0.598 0.545 0.5724083735 168 -0.283 -4.528 -0.419 -0.166 -0.598 0.546 0.5724081498 183 -0.281 -4.528 -0.419 -0.166 -0.598 0.546 0.5724071374 193 -0.281 -4.521 -0.419 -0.166 -0.598 0.546 0.5724039874 194 -0.281 -4.520 -0.419 -0.166 -0.598 0.546 0.5724038461 204 -0.281 -4.519 -0.383 -0.166 -0.598 0.546 0.5722809391 206 -0.281 -4.519 -0.377 -0.166 -0.598 0.546 0.5722772364 217 -0.281 -4.519 -0.377 -0.155 -0.598 0.546 0.5722763019 218 -0.281 -4.519 -0.377 -0.159 -0.598 0.546 0.5722743182 229 -0.281 -4.519 -0.377 -0.159 -0.583 0.546 0.5722623040 230 -0.281 -4.519 -0.377 -0.159 -0.586 0.546 0.5722583634 231 -0.281 -4.519 -0.377 -0.159 -0.588 0.546 0.5722575525 245 -0.281 -4.519 -0.377 -0.159 -0.587 0.547 0.5722575196 254 -0.281 -4.518 -0.369 -0.158 -0.585 0.547 0.5722521583 259 -0.281 -4.518 -0.369 -0.158 -0.585 0.547 0.5722520846 271 -0.287 -4.518 -0.369 -0.158 -0.585 0.547 0.5722476361 272 -0.286 -4.518 -0.369 -0.158 -0.585 0.547 0.5722472097 283 -0.286 -4.517 -0.369 -0.158 -0.585 0.547 0.5722471537 296 -0.286 -4.517 -0.369 -0.158 -0.585 0.548 0.5722448770 297 -0.286 -4.517 -0.369 -0.158 -0.585 0.551 0.5722427910 299 -0.286 -4.517 -0.369 -0.158 -0.585 0.552 0.5722427305 322 -0.286 -4.517 -0.369 -0.158 -0.587 0.552 0.5722423404 324 -0.286 -4.517 -0.369 -0.158 -0.586 0.552 0.5722422118 331 -0.286 -4.516 -0.366 -0.158 -0.586 0.552 0.5722409505 332 -0.286 -4.516 -0.365 -0.157 -0.585 0.552 0.5722409061 335 -0.286 -4.516 -0.365 -0.158 -0.585 0.552 0.5722407453 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.036687 1 -25.0 -25.0 25.0 1.063174 2 -25.0 25.0 -25.0 1.060239 3 -25.0 25.0 25.0 1.079738 4 25.0 -25.0 -25.0 1.043302 5 25.0 -25.0 25.0 1.052769 6 25.0 25.0 -25.0 1.013274 7 25.0 25.0 25.0 1.029804 REL: 8 0.572241 8.378986 1.047373 rel = 0.546358 Number of iterations 3 Min cost was 0.572241 Number of FunctionCalls 338 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.862000 sec Parameters at optimum (transmm) -0.28587 -4.51598 -0.36534 Parameters at optimum (rotdeg) -0.15751 -0.58537 0.55200 Final costs ---------------- Number of surface hits 3040 WM Intensity 816.3783 +/- 220.0579 Ctx Intensity 842.5953 +/- 252.1862 Pct Contrast 1.0153 +/- 22.0147 Cost 0.5722 RelCost 0.8483 Reg at min cost was 1.000 -0.019 0.006 -0.656; -0.010 -0.260 0.965 -41.140; 0.017 0.965 0.261 -2.091; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/003/tmp.bbregister.19926/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.012 0.018 -0.741; -0.020 -0.263 0.965 -36.614; 0.007 0.965 0.263 -1.818; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.007 0.012 -0.085; -0.010 -0.002 -0.001 4.526; -0.010 -0.001 0.002 0.272; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 4.840287 Computing change in rh position Surface RMS Diff (mm) 4.559789 5.307299 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/003/tmp.bbregister.19926/template.nii --init-reg bold/003/tmp.bbregister.19926/bbr.pass1.dat --out-reg bold/003/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/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --cur-reg bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/template.nii --init-reg bold/003/tmp.bbregister.19926/bbr.pass1.dat --out-reg bold/003/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/003/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/003/register.dof6.dat.param --surf white --cur-reg bold/003/tmp.bbregister.19926/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/003/tmp.bbregister.19926/template.nii regfile bold/003/tmp.bbregister.19926/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/003/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 1301635411 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.019 0.006 -0.656; -0.010 -0.260 0.965 -41.140; 0.017 0.965 0.261 -2.091; 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 1.040652 1 -25.0 -25.0 25.0 1.052182 2 -25.0 25.0 -25.0 1.053421 3 -25.0 25.0 25.0 1.066130 4 25.0 -25.0 -25.0 1.031799 5 25.0 -25.0 25.0 1.033509 6 25.0 25.0 -25.0 1.014679 7 25.0 25.0 25.0 1.053279 REL: 8 0.585248 8.345651 1.043206 rel = 0.561009 Initial costs ---------------- Number of surface hits 304441 WM Intensity 818.0911 +/- 216.8722 Ctx Intensity 844.7155 +/- 247.5319 Pct Contrast 1.3158 +/- 21.8138 Cost 0.5852 RelCost 0.5610 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5761 0.5761 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5758 0.5758 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.5757 0.5757 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.5747 0.5747 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5747 0.5747 0.0 13 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.5745 0.5745 0.0 14 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1000 0.5742 0.5742 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.5737 0.5737 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5731 0.5731 0.0 50 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.5731 0.5731 0.0 77 -0.1000 -0.1000 0.1000 0.1000 0.0000 0.1000 0.5728 0.5728 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5726 0.5726 0.0 158 -0.1000 0.0000 0.1000 0.1000 0.0000 0.1000 0.5726 0.5726 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5722 0.5722 0.0 Brute Force -------------------------- Min cost was 0.572241 Number of iterations 729 Search time 1.835000 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 0.026 0.000 0.000 0.000 0.000 0.000 0.5852326668 8 0.025 0.000 0.000 0.000 0.000 0.000 0.5852325405 9 0.023 0.000 0.000 0.000 0.000 0.000 0.5852324609 18 0.023 0.084 0.000 0.000 0.000 0.000 0.5851141412 19 0.023 0.080 0.000 0.000 0.000 0.000 0.5851123709 20 0.023 0.073 0.000 0.000 0.000 0.000 0.5851114647 30 0.023 0.073 -0.001 0.000 0.000 0.000 0.5851114583 38 0.023 0.073 -0.001 -0.144 0.000 0.000 0.5847882060 42 0.023 0.073 -0.001 -0.145 0.000 0.000 0.5847881598 49 0.023 0.073 -0.001 -0.145 -0.078 0.000 0.5847016767 50 0.023 0.073 -0.001 -0.145 -0.057 0.000 0.5846916083 51 0.023 0.073 -0.001 -0.145 -0.059 0.000 0.5846912051 52 0.023 0.073 -0.001 -0.145 -0.061 0.000 0.5846910349 63 0.023 0.073 -0.001 -0.145 -0.063 0.382 0.5833130451 64 0.023 0.073 -0.001 -0.145 -0.063 0.361 0.5832935594 65 0.023 0.073 -0.001 -0.145 -0.063 0.334 0.5832846587 66 0.023 0.073 -0.001 -0.145 -0.063 0.335 0.5832844959 67 0.023 0.073 -0.001 -0.145 -0.063 0.339 0.5832843622 69 0.023 0.073 -0.001 -0.145 -0.063 0.338 0.5832843156 78 0.029 0.073 -0.001 -0.145 -0.063 0.337 0.5832800275 79 0.041 0.073 -0.001 -0.145 -0.063 0.337 0.5832757027 81 0.044 0.073 -0.001 -0.145 -0.063 0.337 0.5832756025 83 0.043 0.073 -0.001 -0.145 -0.063 0.337 0.5832755720 91 0.043 0.118 -0.001 -0.145 -0.063 0.337 0.5832437076 93 0.043 0.119 -0.001 -0.145 -0.063 0.337 0.5832436952 104 0.043 0.119 -0.005 -0.145 -0.063 0.337 0.5832431832 106 0.043 0.119 -0.008 -0.145 -0.063 0.337 0.5832428576 110 0.043 0.119 -0.010 -0.145 -0.063 0.337 0.5832427789 119 0.043 0.119 -0.011 -0.137 -0.063 0.337 0.5832420343 120 0.043 0.119 -0.011 -0.138 -0.063 0.337 0.5832419705 130 0.043 0.119 -0.011 -0.139 -0.041 0.337 0.5832072084 131 0.043 0.119 -0.011 -0.139 -0.025 0.337 0.5831892540 134 0.043 0.119 -0.011 -0.139 -0.014 0.337 0.5831845137 135 0.043 0.119 -0.011 -0.139 -0.013 0.337 0.5831844633 136 0.043 0.119 -0.011 -0.139 -0.012 0.337 0.5831843644 146 0.043 0.119 -0.011 -0.139 -0.012 0.355 0.5831714838 148 0.043 0.119 -0.011 -0.139 -0.012 0.362 0.5831706483 159 0.040 0.119 -0.011 -0.139 -0.012 0.362 0.5831689631 160 0.029 0.119 -0.011 -0.139 -0.012 0.362 0.5831671704 162 0.032 0.119 -0.011 -0.139 -0.012 0.362 0.5831669096 163 0.033 0.119 -0.011 -0.139 -0.012 0.362 0.5831668981 173 0.033 0.120 -0.011 -0.139 -0.012 0.362 0.5831668854 181 0.033 0.120 -0.006 -0.139 -0.012 0.362 0.5831662665 190 0.033 0.120 -0.006 -0.127 -0.012 0.362 0.5831659902 191 0.033 0.120 -0.006 -0.132 -0.012 0.362 0.5831651032 193 0.033 0.120 -0.006 -0.131 -0.012 0.362 0.5831650943 212 0.033 0.120 -0.006 -0.131 -0.012 0.366 0.5831648348 234 0.033 0.119 -0.006 -0.131 -0.012 0.366 0.5831647366 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.037300 1 -25.0 -25.0 25.0 1.053705 2 -25.0 25.0 -25.0 1.052757 3 -25.0 25.0 25.0 1.065191 4 25.0 -25.0 -25.0 1.030781 5 25.0 -25.0 25.0 1.033513 6 25.0 25.0 -25.0 1.016219 7 25.0 25.0 25.0 1.055971 REL: 8 0.583165 8.345436 1.043179 rel = 0.559026 Number of iterations 4 Min cost was 0.583165 Number of FunctionCalls 333 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 49.772000 sec Parameters at optimum (transmm) 0.03353 0.11811 -0.00615 Parameters at optimum (rotdeg) -0.12996 -0.01183 0.36579 Final costs ---------------- Number of surface hits 304441 WM Intensity 819.2857 +/- 215.1194 Ctx Intensity 846.2971 +/- 245.7564 Pct Contrast 1.3837 +/- 21.6186 Cost 0.5832 RelCost 0.5610 Reg at min cost was 1.000 -0.018 -0.001 -0.360; -0.004 -0.258 0.966 -41.030; 0.017 0.966 0.258 -2.004; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/003/register.dof6.dat, type = 14 Original Reg 1.000 -0.019 0.006 -0.656; -0.010 -0.260 0.965 -41.140; 0.017 0.965 0.261 -2.091; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 -0.001 0.006 -0.297; -0.006 -0.002 -0.001 -0.110; -0.000 -0.001 0.002 -0.087; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.243847 Computing change in rh position Surface RMS Diff (mm) 0.307508 0.670787 mri_segreg done Cleaning up Started at Mon Mar 28 17:58:41 EDT 2011 Ended at Mon Mar 28 18:00:31 EDT 2011 BBR-Run-Time-Sec 110 bbregister Done To check results, run: tkregister2 --mov bold/003/template.nii.gz --reg bold/003/register.dof6.dat --surf