Logfile for bbregister Mon Mar 28 18:00:31 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 --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --init-reg-out bold/004/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/004/template.nii.gz bold/004/tmp.bbregister.20148/template.nii mri_convert bold/004/template.nii.gz bold/004/tmp.bbregister.20148/template.nii $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/004/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/004/tmp.bbregister.20148/template.nii... fslregister --s fsf01anat --mov bold/004/tmp.bbregister.20148/template.nii --reg bold/004/tmp.bbregister.20148/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/004/tmp.bbregister.20148/fslregister --dof 6 Log file is bold/004/tmp.bbregister.20148/reg.init.dat.fslregister.log Mon Mar 28 18:00:31 EDT 2011 --s fsf01anat --mov bold/004/tmp.bbregister.20148/template.nii --reg bold/004/tmp.bbregister.20148/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/fslregister/refvol.fslregister.nii mri_convert /space/freesurfer/subjects/fsfast-tutorial.v5.1-subjects/fsf01anat/mri/brainmask.mgz bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 mri_convert bold/004/tmp.bbregister.20148/template.nii bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/004/tmp.bbregister.20148/template.nii bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.180 2011/03/21 23:37:29 mreuter Exp $ reading from bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii movable volume bold/004/tmp.bbregister.20148/template.nii reg file bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii --reg bold/004/tmp.bbregister.20148/fslregister/reg0.20182.dat --regheader --fslregout bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii reg file bold/004/tmp.bbregister.20148/fslregister/reg0.20182.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/004/tmp.bbregister.20148/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 18:00:34 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/004/tmp.bbregister.20148/fslregister/refvol.fslregister.nii -in bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/004/tmp.bbregister.20148/fslregister/fslmat0.trans.mat -schedule /usr/pubsw/packages/fsl/4.1.4/etc/flirtsch/xyztrans.sch -init bold/004/tmp.bbregister.20148/reg.init.dat.fsl.mat0 Mon Mar 28 18:00:42 EDT 2011 /autofs/space/crash_002/users/greve/mytmp/fsftutv5.1/sess01 flirt.fsl -ref bold/004/tmp.bbregister.20148/fslregister/refvol.fslregister.nii -in bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/004/tmp.bbregister.20148/reg.init.dat.fsl.mat -init bold/004/tmp.bbregister.20148/fslregister/fslmat0.trans.mat -schedule /space/crash/1/users/greve/freesurferx86/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s fsf01anat --mov bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii --reg bold/004/tmp.bbregister.20148/reg.init.dat --fslreg bold/004/tmp.bbregister.20148/reg.init.dat.fsl.mat --noedit tkregister_tcl /space/crash/1/users/greve/freesurferx86/tktools/tkregister2.tcl ---- FSL registration matrix -------- -1.000 0.013 0.021 231.356; -0.017 0.258 -0.966 138.033; -0.018 -0.966 -0.258 247.883; 0.000 0.000 0.000 1.000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/004/tmp.bbregister.20148/fslregister/movvol.fslregister.nii reg file bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/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 0.018 -0.017 4.336; -0.021 -0.258 0.966 -36.538; 0.013 0.966 0.258 -1.852; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 0.018 -0.017 4.336; -0.021 -0.258 0.966 -36.538; 0.013 0.966 0.258 -1.852; 0.000 0.000 0.000 1.000; Determinant 1 subject = fsf01anat RegMat --------------------------- -1.000 0.018 -0.017 4.336; -0.021 -0.258 0.966 -36.538; 0.013 0.966 0.258 -1.852; 0.000 0.000 0.000 1.000; mri_matrix_multiply -im bold/004/tmp.bbregister.20148/fslregister/swapreg.dat -im bold/004/tmp.bbregister.20148/reg.init.dat -om bold/004/tmp.bbregister.20148/reg.init.dat Started at Mon Mar 28 18:00:31 EDT 2011 Ended at Mon Mar 28 18:00:59 EDT 2011 fslregister Done To check results, run: tkregister2 --mov bold/004/tmp.bbregister.20148/template.nii --reg bold/004/tmp.bbregister.20148/reg.init.dat --surf orig mri_segreg --mov bold/004/tmp.bbregister.20148/template.nii --init-reg bold/004/tmp.bbregister.20148/reg.init.dat --out-reg bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/template.nii --init-reg bold/004/tmp.bbregister.20148/reg.init.dat --out-reg bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/template.nii regfile bold/004/tmp.bbregister.20148/reg.init.dat subject fsf01anat dof 6 outregfile bold/004/tmp.bbregister.20148/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 1302347341 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.018 0.017 -0.898; -0.021 -0.258 0.966 -36.538; 0.013 0.966 0.258 -1.852; 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 1.073896 1 -25.0 -25.0 25.0 1.041397 2 -25.0 25.0 -25.0 1.070844 3 -25.0 25.0 25.0 1.070696 4 25.0 -25.0 -25.0 1.083204 5 25.0 -25.0 25.0 1.061084 6 25.0 25.0 -25.0 1.030853 7 25.0 25.0 25.0 1.062804 REL: 8 0.926214 8.494776 1.061847 rel = 0.872267 Initial costs ---------------- Number of surface hits 3040 WM Intensity 875.3319 +/- 201.8983 Ctx Intensity 850.5143 +/- 233.6363 Pct Contrast -4.8063 +/- 23.0614 Cost 0.9262 RelCost 0.8723 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 1.0138 1.0138 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9779 0.9779 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9674 0.9674 0.0 9 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 0.9491 0.9491 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9230 0.9230 0.0 27 -4.0000 -4.0000 0.0000 -4.0000 -4.0000 -4.0000 0.9079 0.9079 0.0 30 -4.0000 -4.0000 0.0000 -4.0000 0.0000 -4.0000 0.8882 0.8882 0.0 36 -4.0000 -4.0000 0.0000 0.0000 -4.0000 -4.0000 0.8719 0.8719 0.0 40 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.8629 0.8629 0.0 256 0.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.8497 0.8497 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7451 0.7451 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6341 0.6341 0.0 Brute Force -------------------------- Min cost was 0.634120 Number of iterations 729 Search time 1.902000 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 5 -0.618 -4.000 0.000 0.000 0.000 0.000 0.6301620531 7 -0.562 -4.000 0.000 0.000 0.000 0.000 0.6299952545 8 -0.390 -4.000 0.000 0.000 0.000 0.000 0.6293082208 11 -0.414 -4.000 0.000 0.000 0.000 0.000 0.6292723447 12 -0.417 -4.000 0.000 0.000 0.000 0.000 0.6292719227 13 -0.418 -4.000 0.000 0.000 0.000 0.000 0.6292718182 16 -0.420 -4.000 0.000 0.000 0.000 0.000 0.6292717100 18 -0.419 -4.000 0.000 0.000 0.000 0.000 0.6292716482 21 -0.419 -5.618 0.000 0.000 0.000 0.000 0.6167845490 22 -0.419 -5.072 0.000 0.000 0.000 0.000 0.6077436119 27 -0.419 -5.142 0.000 0.000 0.000 0.000 0.6075575994 28 -0.419 -5.139 0.000 0.000 0.000 0.000 0.6075571537 30 -0.419 -5.140 0.000 0.000 0.000 0.000 0.6075569633 37 -0.419 -5.140 -0.243 0.000 0.000 0.000 0.6070718218 38 -0.419 -5.140 -0.181 0.000 0.000 0.000 0.6068753853 39 -0.419 -5.140 -0.157 0.000 0.000 0.000 0.6068733234 40 -0.419 -5.140 -0.168 0.000 0.000 0.000 0.6068705249 43 -0.419 -5.140 -0.170 0.000 0.000 0.000 0.6068702110 50 -0.419 -5.140 -0.169 -0.618 0.000 0.000 0.5995032130 52 -0.419 -5.140 -0.169 -0.524 0.000 0.000 0.5987814206 53 -0.419 -5.140 -0.169 -0.350 0.000 0.000 0.5984236706 54 -0.419 -5.140 -0.169 -0.387 0.000 0.000 0.5981156988 55 -0.419 -5.140 -0.169 -0.423 0.000 0.000 0.5980573284 56 -0.419 -5.140 -0.169 -0.414 0.000 0.000 0.5980417363 57 -0.419 -5.140 -0.169 -0.411 0.000 0.000 0.5980403979 58 -0.419 -5.140 -0.169 -0.410 0.000 0.000 0.5980401331 66 -0.419 -5.140 -0.169 -0.410 -0.618 0.000 0.5903097323 68 -0.419 -5.140 -0.169 -0.410 -0.535 0.000 0.5899323803 69 -0.419 -5.140 -0.169 -0.410 -0.477 0.000 0.5898693374 70 -0.419 -5.140 -0.169 -0.410 -0.484 0.000 0.5898586693 71 -0.419 -5.140 -0.169 -0.410 -0.495 0.000 0.5898548917 74 -0.419 -5.140 -0.169 -0.410 -0.501 0.000 0.5898543974 75 -0.419 -5.140 -0.169 -0.410 -0.498 0.000 0.5898541567 79 -0.419 -5.140 -0.169 -0.410 -0.498 1.000 0.5826063739 84 -0.419 -5.140 -0.169 -0.410 -0.498 0.887 0.5818132726 86 -0.419 -5.140 -0.169 -0.410 -0.498 0.873 0.5818021298 88 -0.419 -5.140 -0.169 -0.410 -0.498 0.874 0.5818020934 90 -0.419 -5.140 -0.169 -0.410 -0.498 0.875 0.5818019795 99 -0.297 -5.140 -0.169 -0.410 -0.498 0.875 0.5817508779 100 -0.345 -5.140 -0.169 -0.410 -0.498 0.875 0.5814747880 101 -0.356 -5.140 -0.169 -0.410 -0.498 0.875 0.5814573418 102 -0.363 -5.140 -0.169 -0.410 -0.498 0.875 0.5814529740 110 -0.363 -4.758 -0.169 -0.410 -0.498 0.875 0.5790178840 112 -0.363 -4.868 -0.169 -0.410 -0.498 0.875 0.5784830700 114 -0.363 -4.854 -0.169 -0.410 -0.498 0.875 0.5784662799 115 -0.363 -4.848 -0.169 -0.410 -0.498 0.875 0.5784647749 124 -0.363 -4.848 -0.467 -0.410 -0.498 0.875 0.5774569123 125 -0.363 -4.848 -0.455 -0.410 -0.498 0.875 0.5774546050 127 -0.363 -4.848 -0.457 -0.410 -0.498 0.875 0.5774544348 129 -0.363 -4.848 -0.458 -0.410 -0.498 0.875 0.5774543349 130 -0.363 -4.848 -0.459 -0.410 -0.498 0.875 0.5774543240 137 -0.363 -4.848 -0.459 -0.644 -0.498 0.875 0.5770900095 138 -0.363 -4.848 -0.459 -0.593 -0.498 0.875 0.5765862495 139 -0.363 -4.848 -0.459 -0.540 -0.498 0.875 0.5764348578 140 -0.363 -4.848 -0.459 -0.545 -0.498 0.875 0.5764311923 141 -0.363 -4.848 -0.459 -0.547 -0.498 0.875 0.5764306453 150 -0.363 -4.848 -0.459 -0.547 -0.469 0.875 0.5761483328 151 -0.363 -4.848 -0.459 -0.547 -0.395 0.875 0.5760720280 153 -0.363 -4.848 -0.459 -0.547 -0.426 0.875 0.5759557564 154 -0.363 -4.848 -0.459 -0.547 -0.428 0.875 0.5759557521 162 -0.363 -4.848 -0.459 -0.547 -0.428 1.043 0.5754667419 164 -0.363 -4.848 -0.459 -0.547 -0.428 0.986 0.5751742033 166 -0.363 -4.848 -0.459 -0.547 -0.428 0.969 0.5751404843 167 -0.363 -4.848 -0.459 -0.547 -0.428 0.967 0.5751403834 181 -0.368 -4.848 -0.459 -0.547 -0.428 0.967 0.5751346925 182 -0.369 -4.848 -0.459 -0.547 -0.428 0.967 0.5751342064 183 -0.370 -4.848 -0.459 -0.547 -0.428 0.967 0.5751341102 206 -0.370 -4.848 -0.500 -0.547 -0.428 0.967 0.5750002110 208 -0.370 -4.848 -0.504 -0.547 -0.428 0.967 0.5749961547 209 -0.370 -4.848 -0.513 -0.547 -0.428 0.967 0.5749894904 212 -0.370 -4.848 -0.516 -0.547 -0.428 0.967 0.5749884612 213 -0.370 -4.848 -0.517 -0.547 -0.428 0.967 0.5749882105 214 -0.370 -4.848 -0.519 -0.547 -0.428 0.967 0.5749879446 215 -0.370 -4.848 -0.520 -0.547 -0.428 0.967 0.5749878595 224 -0.370 -4.848 -0.520 -0.559 -0.428 0.967 0.5749483555 225 -0.370 -4.848 -0.520 -0.571 -0.428 0.967 0.5749453267 226 -0.370 -4.848 -0.520 -0.566 -0.428 0.967 0.5749421335 228 -0.370 -4.848 -0.520 -0.565 -0.428 0.967 0.5749420788 238 -0.370 -4.848 -0.520 -0.565 -0.434 0.967 0.5748965656 239 -0.370 -4.848 -0.520 -0.565 -0.451 0.967 0.5748509789 251 -0.370 -4.848 -0.520 -0.565 -0.450 0.987 0.5748306574 252 -0.370 -4.848 -0.520 -0.565 -0.450 0.984 0.5748271084 253 -0.370 -4.848 -0.520 -0.565 -0.450 0.981 0.5748244537 267 -0.372 -4.848 -0.520 -0.565 -0.450 0.981 0.5748243560 280 -0.372 -4.849 -0.520 -0.565 -0.450 0.981 0.5748240862 281 -0.372 -4.850 -0.520 -0.565 -0.450 0.981 0.5748240194 291 -0.372 -4.850 -0.524 -0.565 -0.450 0.981 0.5748238846 295 -0.372 -4.850 -0.528 -0.565 -0.450 0.981 0.5748238470 296 -0.372 -4.850 -0.526 -0.565 -0.450 0.981 0.5748238107 297 -0.372 -4.850 -0.527 -0.565 -0.450 0.981 0.5748237567 307 -0.372 -4.850 -0.527 -0.567 -0.450 0.981 0.5748230185 309 -0.372 -4.850 -0.527 -0.568 -0.450 0.981 0.5748229691 320 -0.372 -4.850 -0.527 -0.568 -0.453 0.981 0.5748212885 334 -0.372 -4.850 -0.527 -0.568 -0.452 0.986 0.5748157099 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 1.032606 1 -25.0 -25.0 25.0 1.055633 2 -25.0 25.0 -25.0 1.057265 3 -25.0 25.0 25.0 1.067066 4 25.0 -25.0 -25.0 1.054141 5 25.0 -25.0 25.0 1.043216 6 25.0 25.0 -25.0 1.014296 7 25.0 25.0 25.0 1.031718 REL: 8 0.574816 8.355942 1.044493 rel = 0.55033 Number of iterations 3 Min cost was 0.574816 Number of FunctionCalls 337 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.905000 sec Parameters at optimum (transmm) -0.37162 -4.85027 -0.52713 Parameters at optimum (rotdeg) -0.56846 -0.45222 0.98590 Final costs ---------------- Number of surface hits 3040 WM Intensity 817.1486 +/- 221.4343 Ctx Intensity 844.1619 +/- 253.9893 Pct Contrast 1.1118 +/- 22.1415 Cost 0.5748 RelCost 0.8723 Reg at min cost was 1.000 -0.021 -0.002 -0.629; -0.003 -0.249 0.969 -41.414; 0.021 0.968 0.249 -2.023; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/004/tmp.bbregister.20148/bbr.pass1.dat, type = 14 Original Reg 1.000 -0.018 0.017 -0.898; -0.021 -0.258 0.966 -36.538; 0.013 0.966 0.258 -1.852; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.000 0.003 0.019 -0.269; -0.017 -0.009 -0.003 4.877; -0.008 -0.002 0.009 0.172; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 5.427248 Computing change in rh position Surface RMS Diff (mm) 4.934955 6.460689 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/004/tmp.bbregister.20148/template.nii --init-reg bold/004/tmp.bbregister.20148/bbr.pass1.dat --out-reg bold/004/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/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --cur-reg bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/template.nii --init-reg bold/004/tmp.bbregister.20148/bbr.pass1.dat --out-reg bold/004/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/004/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/004/register.dof6.dat.param --surf white --cur-reg bold/004/tmp.bbregister.20148/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/004/tmp.bbregister.20148/template.nii regfile bold/004/tmp.bbregister.20148/bbr.pass1.dat subject fsf01anat dof 6 outregfile bold/004/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 1301651875 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 1.000 -0.021 -0.002 -0.629; -0.003 -0.249 0.969 -41.414; 0.021 0.968 0.249 -2.023; 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 1.037374 1 -25.0 -25.0 25.0 1.045380 2 -25.0 25.0 -25.0 1.055517 3 -25.0 25.0 25.0 1.063528 4 25.0 -25.0 -25.0 1.038236 5 25.0 -25.0 25.0 1.028927 6 25.0 25.0 -25.0 1.020221 7 25.0 25.0 25.0 1.050536 REL: 8 0.578137 8.339719 1.042465 rel = 0.554587 Initial costs ---------------- Number of surface hits 304441 WM Intensity 818.7022 +/- 218.3653 Ctx Intensity 846.5592 +/- 250.0001 Pct Contrast 1.3936 +/- 22.1369 Cost 0.5781 RelCost 0.5546 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.5787 0.5787 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.5779 0.5779 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.5774 0.5774 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.5770 0.5770 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.5768 0.5768 0.0 11 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1000 0.5760 0.5760 0.0 41 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.1000 0.5760 0.5760 0.0 92 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.5759 0.5759 0.0 95 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.1000 0.5759 0.5759 0.0 119 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1000 0.5758 0.5758 0.0 122 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1000 0.5755 0.5755 0.0 293 0.0000 -0.1000 0.0000 0.1000 0.0000 0.1000 0.5754 0.5754 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.5753 0.5753 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.5748 0.5748 0.0 682 0.1000 0.1000 0.0000 -0.1000 0.1000 0.0000 0.5747 0.5747 0.0 709 0.1000 0.1000 0.1000 -0.1000 0.1000 0.0000 0.5746 0.5746 0.0 Brute Force -------------------------- Min cost was 0.574584 Number of iterations 729 Search time 1.912000 sec Parameters at best (transmm, rotdeg) 0.100 0.100 0.100 -0.100 0.100 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0.1 1 0.1 2 0.1 3 -0.1 4 0.1 5 0 7 0.058 0.100 0.100 -0.100 0.100 0.000 0.5781066849 9 0.055 0.100 0.100 -0.100 0.100 0.000 0.5781063198 10 0.054 0.100 0.100 -0.100 0.100 0.000 0.5781062940 17 0.054 0.482 0.100 -0.100 0.100 0.000 0.5779630731 18 0.054 0.300 0.100 -0.100 0.100 0.000 0.5772154843 29 0.054 0.301 0.076 -0.100 0.100 0.000 0.5772096474 30 0.054 0.301 0.083 -0.100 0.100 0.000 0.5772085331 31 0.054 0.301 0.082 -0.100 0.100 0.000 0.5772084844 41 0.054 0.301 0.081 -0.131 0.100 0.000 0.5771657927 42 0.054 0.301 0.081 -0.154 0.100 0.000 0.5771585554 53 0.054 0.301 0.081 -0.155 -0.180 0.000 0.5750321699 55 0.054 0.301 0.081 -0.155 -0.181 0.000 0.5750321518 57 0.054 0.301 0.081 -0.155 -0.182 0.000 0.5750321464 62 0.054 0.301 0.081 -0.155 -0.183 0.000 0.5750320777 69 0.054 0.301 0.081 -0.155 -0.183 0.096 0.5748920804 70 0.054 0.301 0.081 -0.155 -0.183 0.104 0.5748911492 74 0.054 0.301 0.081 -0.155 -0.183 0.103 0.5748910562 82 0.007 0.301 0.081 -0.155 -0.183 0.103 0.5748395480 84 0.003 0.301 0.081 -0.155 -0.183 0.103 0.5748392780 86 0.004 0.301 0.081 -0.155 -0.183 0.103 0.5748392762 95 0.005 0.304 0.081 -0.155 -0.183 0.103 0.5748378547 96 0.005 0.311 0.081 -0.155 -0.183 0.103 0.5748373829 98 0.005 0.309 0.081 -0.155 -0.183 0.103 0.5748372114 107 0.005 0.309 0.038 -0.155 -0.183 0.103 0.5747602464 108 0.005 0.309 0.022 -0.155 -0.183 0.103 0.5747598613 109 0.005 0.309 0.030 -0.155 -0.183 0.103 0.5747582550 120 0.005 0.309 0.029 -0.116 -0.183 0.103 0.5747311550 121 0.005 0.309 0.029 -0.118 -0.183 0.103 0.5747301980 122 0.005 0.309 0.029 -0.124 -0.183 0.103 0.5747288112 124 0.005 0.309 0.029 -0.126 -0.183 0.103 0.5747286925 125 0.005 0.309 0.029 -0.127 -0.183 0.103 0.5747286492 134 0.005 0.309 0.029 -0.127 -0.182 0.103 0.5747285612 135 0.005 0.309 0.029 -0.127 -0.180 0.103 0.5747284228 155 0.008 0.309 0.029 -0.127 -0.180 0.103 0.5747283431 164 0.009 0.310 0.029 -0.127 -0.180 0.103 0.5747278866 165 0.009 0.320 0.029 -0.127 -0.180 0.103 0.5747264316 167 0.009 0.317 0.029 -0.127 -0.180 0.103 0.5747261633 176 0.009 0.316 0.032 -0.127 -0.180 0.103 0.5747254298 179 0.009 0.316 0.033 -0.127 -0.180 0.103 0.5747254165 188 0.009 0.316 0.033 -0.126 -0.180 0.103 0.5747253778 206 0.009 0.316 0.033 -0.126 -0.180 0.106 0.5747252890 272 0.009 0.316 0.033 -0.126 -0.180 0.107 0.5747252363 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 1.037200 1 -25.0 -25.0 25.0 1.048324 2 -25.0 25.0 -25.0 1.056337 3 -25.0 25.0 25.0 1.062961 4 25.0 -25.0 -25.0 1.038858 5 25.0 -25.0 25.0 1.030406 6 25.0 25.0 -25.0 1.020636 7 25.0 25.0 25.0 1.050899 REL: 8 0.574725 8.345621 1.043203 rel = 0.550924 Number of iterations 4 Min cost was 0.574725 Number of FunctionCalls 332 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 53.442000 sec Parameters at optimum (transmm) 0.00864 0.31617 0.03300 Parameters at optimum (rotdeg) -0.12612 -0.18003 0.10749 Final costs ---------------- Number of surface hits 304441 WM Intensity 821.6865 +/- 215.1370 Ctx Intensity 850.2736 +/- 246.7786 Pct Contrast 1.5262 +/- 21.7301 Cost 0.5747 RelCost 0.5546 Reg at min cost was 1.000 -0.024 -0.005 -0.536; -0.002 -0.247 0.969 -41.104; 0.024 0.969 0.247 -1.901; 0.000 0.000 0.000 1.000; Writing optimal reg to bold/004/register.dof6.dat, type = 14 Original Reg 1.000 -0.021 -0.002 -0.629; -0.003 -0.249 0.969 -41.414; 0.021 0.968 0.249 -2.023; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg 0.000 0.003 0.003 -0.092; -0.002 -0.002 -0.001 -0.311; -0.003 -0.000 0.002 -0.122; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 0.316625 Computing change in rh position Surface RMS Diff (mm) 0.375701 0.642939 mri_segreg done Cleaning up Started at Mon Mar 28 18:00:31 EDT 2011 Ended at Mon Mar 28 18:02:24 EDT 2011 BBR-Run-Time-Sec 113 bbregister Done To check results, run: tkregister2 --mov bold/004/template.nii.gz --reg bold/004/register.dof6.dat --surf