Logfile for bbregister Sun Apr 1 20:44:56 EDT 2012 setenv SUBJECTS_DIR /home/kayhan/test/myproject/control001/tp1 cd /home/kayhan/test/myproject/control001/tp1/NIFTI /opt/freesurfer/bin/bbregister --mov fMRI.nii.gz --bold --s FREESURFER --init-spm --reg bbregister/fmri-TO-orig.dat --fslmat bbregister/fmri-TO-orig.mat $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux sbia-pc71 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_convert fMRI.nii.gz bbregister/tmp.bbregister.822/template.nii mri_convert fMRI.nii.gz bbregister/tmp.bbregister.822/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from fMRI.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to bbregister/tmp.bbregister.822/template.nii... spmregister --s FREESURFER --mov bbregister/tmp.bbregister.822/template.nii --reg bbregister/tmp.bbregister.822/reg.init.dat --tmp bbregister/tmp.bbregister.822/spmregister Log file is bbregister/tmp.bbregister.822/spmregister.log Sun Apr 1 20:44:58 EDT 2012 --s FREESURFER --mov bbregister/tmp.bbregister.822/template.nii --reg bbregister/tmp.bbregister.822/reg.init.dat --tmp bbregister/tmp.bbregister.822/spmregister $Id: spmregister,v 1.39 2011/03/02 20:16:40 nicks Exp $ matlab matlab fmt img UseSPMGetSpace 1 -------------------------------------- /home/kayhan/test/myproject/control001/tp1/NIFTI mri_convert /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/brainmask.mgz bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img -ic 0 0 0 mri_convert /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/brainmask.mgz bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img -ic 0 0 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img... Analyze Output Matrix -1.000 0.000 0.000 129.000; 0.000 0.000 1.000 -129.000; 0.000 -1.000 0.000 129.000; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 -------------------------------------- /home/kayhan/test/myproject/control001/tp1/NIFTI mri_convert bbregister/tmp.bbregister.822/template.nii bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img -ic 0 0 0 --frame 0 mri_convert bbregister/tmp.bbregister.822/template.nii bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img -ic 0 0 0 --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bbregister/tmp.bbregister.822/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) keeping frame 0 writing to bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img... Analyze Output Matrix -3.125 -0.000 -0.000 103.125; -0.000 3.125 -0.000 -103.125; 0.000 0.000 4.200 -73.500; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Matlab file is bbregister/tmp.bbregister.822/spmregister/spmregister.862.m monly = 0; targvol = 'bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img'; srcvol = 'bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img'; errfile = 'bbregister/tmp.bbregister.822/spmregister/spmregister.862.err'; if(exist('spm_coreg') ~= 2) fprintf('ERROR: cannot find spm_coreg.m. Make sure that the SPM\n'); fprintf(' package is in your matlab path (check ~/matlab/startup)\n'); fp = fopen(errfile,'w'); fprintf(fp,'ERROR: cannot find spm_coreg.m. Make sure that the SPM\n'); fprintf(fp,' package is in your matlab path (check ~/matlab/startup)\n'); fclose(fp); return; quit; end which spm_coreg global defaults spm_defaults % load spm2's default fields fprintf('INFO: Assuming RAS coordinate system\n'); defaults.analyze.flip = 0; %=========================================================================== % coregistration defaults %=========================================================================== defaults.coreg.estimate.cost_fun = 'nmi'; defaults.coreg.estimate.sep = [4 2]; defaults.coreg.estimate.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001]; defaults.coreg.estimate.fwhm = [7 7]; defaults.coreg.estimate.params = [0 0 0 0 0 0]; defaults.coreg.estimate.graphics = 0; % dont crate ps file %=========================================================================== % coregister files %=========================================================================== disp(sprintf('using %s as the target image',targvol)); disp(sprintf('using %s as the source image',srcvol)); [pth1,nam1,ext1] = fileparts(deblank(targvol)); [pth2,nam2,ext2] = fileparts(deblank(srcvol)); %tmp = spm_get('Files',pth1,[nam1 ext1]); tmp = sprintf('%s/%s%s',pth1,nam1,ext1); VG = spm_vol(tmp); % target image if(isempty(VG)) fprintf('ERROR: loading target %s\n',targvol); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: loading target %s\n',targvol); fclose(fp); return; quit; end % tmp = spm_get('Files',pth2,[nam2 ext2]) tmp = sprintf('%s/%s%s',pth2,nam2,ext2); VF = spm_vol(tmp); % source image if(isempty(VF)) fprintf('ERROR: loading source %s\n',srcvol); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: loading source %s\n',srcvol); fclose(fp); return; quit; end fprintf('\n\nINFO: ignore warnings about scalefactor\n\n'); disp('determining coregistration parameters...') tic; try x = spm_coreg(VG.fname,VF.fname,defaults.coreg.estimate); catch fprintf('ERROR: spm_coreg\n'); fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg\n'); fprintf(fp,'%s\n',which('spm_coreg')); fclose(fp); return; quit; end if(isempty(x)) fprintf('ERROR: spm_coreg\n'); if(~monly) fp = fopen(errfile,'a'); fprintf(fp,'ERROR: spm_coreg\n'); fclose(fp); return; quit; end end fprintf('Finished after %g sec\n',toc); fprintf('Parameters '); fprintf('%g ',x); fprintf('\n'); %---------write out the .mat file---see spm_coreg_ui.m line 283 M = inv(spm_matrix(x)); if(1) fprintf('Using spm_get_space\n'); MM = zeros(4,4,1); MM = spm_get_space(deblank(VF.fname)); spm_get_space(deblank(VF.fname), M*MM); fprintf('\n\nINFO: ignore warnings about scalefactor\n\n'); else fprintf('Using MRIread/write instead of spm_get_space\n'); ff = MRIread(deblank(VF.fname)); ff.vox2ras1 = M*ff.vox2ras1; ff.vox2ras0 = vox2ras_1to0(ff.vox2ras1); ff.vox2ras = ff.vox2ras0; MRIwrite(ff,deblank(VF.fname)); end return; if(~monly) quit; end Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. Warning: No window system found. Java option 'MWT' ignored < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.9.0.529 (R2009b) 64-bit (glnxa64) August 12, 2009 {Warning: Duplicate directory name: /home/kayhan/matlab.} To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> /usr/share/spm8/spm_coreg.m >> >> >> Direct calls to spm_defauts are deprecated. Please use spm('Defaults',modality) or spm_get_defaults instead. >> >> INFO: Assuming RAS coordinate system >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> using bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img as the target image >> using bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img as the source image >> >> >> >> >> >> >> >> >> >> >> >> >> >> INFO: ignore warnings about scalefactor >> >> determining coregistration parameters... >> >> >> iteration 1... 1.047 0 0 0 0 0 | -1.0547 1.047 -10.44 0 0 0 0 | -1.0737 1.047 -10.44 -1.567 0 0 0 | -1.075 1.047 -10.44 -1.567 -0.01643 0 0 | -1.0751 1.047 -10.44 -1.567 -0.01643 0 0 | -1.0751 1.047 -10.44 -1.567 -0.01643 0 0.008849 | -1.0752 iteration 2... 0.7332 -10.44 -1.567 -0.01643 0 0.008849 | -1.0753 0.7332 -10.35 -1.567 -0.01643 0 0.008849 | -1.0753 0.7332 -10.35 -1.497 -0.01643 0 0.008849 | -1.0753 0.7332 -10.35 -1.497 -0.01748 0 0.008849 | -1.0753 0.7332 -10.35 -1.497 -0.01748 0.005562 0.008849 | -1.0753 0.7332 -10.35 -1.497 -0.01748 0.005562 0.006548 | -1.0753 iteration 3... 0.6791 -10.35 -1.497 -0.01748 0.005562 0.006548 | -1.0754 0.6791 -10.33 -1.497 -0.01748 0.005562 0.006548 | -1.0754 0.6791 -10.33 -1.495 -0.01748 0.005562 0.006548 | -1.0754 0.6791 -10.33 -1.495 -0.01748 0.005562 0.006548 | -1.0754 0.6791 -10.33 -1.495 -0.01748 0.005562 0.006548 | -1.0754 0.6791 -10.33 -1.495 -0.01748 0.005562 0.006361 | -1.0754 iteration 4... 0.6791 -10.33 -1.495 -0.01748 0.005562 0.006361 | -1.0754 0.6791 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0754 0.6791 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0754 0.6791 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0754 0.6791 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0754 0.6791 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0754 iteration 1... 0.5732 -10.34 -1.495 -0.01748 0.005562 0.006361 | -1.0749 0.5732 -10.46 -1.495 -0.01748 0.005562 0.006361 | -1.0749 0.5732 -10.46 -1.422 -0.01748 0.005562 0.006361 | -1.0749 0.5732 -10.46 -1.422 -0.02212 0.005562 0.006361 | -1.075 0.5732 -10.46 -1.422 -0.02212 0.005562 0.006361 | -1.075 0.5732 -10.46 -1.422 -0.02212 0.005562 0.002826 | -1.075 iteration 2... 0.5383 -10.46 -1.422 -0.02212 0.005562 0.002826 | -1.075 0.5383 -10.41 -1.422 -0.02212 0.005562 0.002826 | -1.075 0.5383 -10.41 -1.422 -0.02212 0.005562 0.002826 | -1.075 0.5383 -10.41 -1.422 -0.02214 0.005562 0.002826 | -1.075 0.5383 -10.41 -1.422 -0.02214 0.005562 0.002826 | -1.075 0.5383 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 iteration 3... 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 0.5252 -10.41 -1.422 -0.02214 0.005562 0.00155 | -1.075 >> >> Finished after 16.7957 sec >> >> Parameters >> 0.525196 -10.4059 -1.42221 -0.0221354 0.00556191 0.0015495 >> >> >> >> >> >> >> Using spm_get_space INFO: ignore warnings about scalefactor >> >> >> -------------------------------------------------- /home/kayhan/test/myproject/control001/tp1/NIFTI tkregister2_cmdl --s FREESURFER --mov bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img --regheader --noedit --reg bbregister/tmp.bbregister.822/reg.init.dat --targ bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img --mgz tkregister_tcl /opt/freesurfer/tktools/tkregister2.tcl target volume bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img movable volume bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img reg file bbregister/tmp.bbregister.822/reg.init.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target bbregister/tmp.bbregister.822/spmregister/refvol.spmregister.img 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 bbregister/tmp.bbregister.822/spmregister/movvol.spmregister.img Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 4.200 -69.300; 0.000 -3.125 0.000 100.000; 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 -0.002 -0.006 -0.525; -0.006 0.022 1.000 -1.422; 0.001 -1.000 0.022 10.406; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -1.000 -0.002 -0.006 -0.525; -0.006 0.022 1.000 -1.422; 0.001 -1.000 0.022 10.406; 0.000 0.000 0.000 1.000; Determinant -1 subject = FREESURFER RegMat --------------------------- -1.000 -0.002 -0.006 -0.525; -0.006 0.022 1.000 -1.422; 0.001 -1.000 0.022 10.406; 0.000 0.000 0.000 1.000; Started at Sun Apr 1 20:44:58 EDT 2012 Ended at Sun Apr 1 20:45:19 EDT 2012 spmregister Done To check results, run: tkregister2 --mov bbregister/tmp.bbregister.822/template.nii --reg bbregister/tmp.bbregister.822/reg.init.dat --surf orig mri_segreg --mov bbregister/tmp.bbregister.822/template.nii --init-reg bbregister/tmp.bbregister.822/reg.init.dat --out-reg bbregister/tmp.bbregister.822/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 /home/kayhan/test/myproject/control001/tp1 cd /home/kayhan/test/myproject/control001/tp1/NIFTI mri_segreg --mov bbregister/tmp.bbregister.822/template.nii --init-reg bbregister/tmp.bbregister.822/reg.init.dat --out-reg bbregister/tmp.bbregister.822/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 sbia-pc71 machine x86_64 user kayhan movvol bbregister/tmp.bbregister.822/template.nii regfile bbregister/tmp.bbregister.822/reg.init.dat subject FREESURFER dof 6 outregfile bbregister/tmp.bbregister.822/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 1333561382 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.000 -0.002 -0.006 -0.525; -0.006 0.022 1.000 -1.422; 0.001 -1.000 0.022 10.406; 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 Computing relative cost 0 -25.0 -25.0 -25.0 1.062941 1 -25.0 -25.0 25.0 1.068057 2 -25.0 25.0 -25.0 1.105561 3 -25.0 25.0 25.0 1.071003 4 25.0 -25.0 -25.0 1.062343 5 25.0 -25.0 25.0 1.006743 6 25.0 25.0 -25.0 1.038952 7 25.0 25.0 25.0 1.033594 REL: 8 1.004688 8.449194 1.056149 rel = 0.951275 Initial costs ---------------- Number of surface hits 2593 WM Intensity 855.8862 +/- 205.8648 Ctx Intensity 838.0680 +/- 234.9062 Pct Contrast -4.0719 +/- 25.3330 Cost 1.0047 RelCost 0.9513 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 0.9971 0.9971 0.0 10 -4.0000 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.9838 0.9838 0.0 13 -4.0000 -4.0000 -4.0000 0.0000 0.0000 0.0000 0.9686 0.9686 0.0 287 0.0000 -4.0000 0.0000 0.0000 4.0000 4.0000 0.9504 0.9504 0.0 539 4.0000 -4.0000 0.0000 4.0000 4.0000 4.0000 0.9502 0.9502 0.0 Brute Force -------------------------- Min cost was 0.950242 Number of iterations 729 Search time 1.287000 sec Parameters at best (transmm, rotdeg) 4.000 -4.000 0.000 4.000 4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 4 1 -4 2 0 3 4 4 4 5 4 12 3.984 -4.000 0.000 4.000 4.000 4.000 0.9502189876 13 3.982 -4.000 0.000 4.000 4.000 4.000 0.9502179768 18 3.982 -3.000 0.000 4.000 4.000 4.000 0.9444440900 22 3.982 -3.382 0.000 4.000 4.000 4.000 0.9402224713 24 3.982 -3.369 0.000 4.000 4.000 4.000 0.9402063959 26 3.982 -3.365 0.000 4.000 4.000 4.000 0.9402054952 32 3.982 -3.364 1.000 4.000 4.000 4.000 0.9375423442 36 3.982 -3.364 0.618 4.000 4.000 4.000 0.9349167500 37 3.982 -3.364 0.665 4.000 4.000 4.000 0.9348510991 39 3.982 -3.364 0.654 4.000 4.000 4.000 0.9348457311 40 3.982 -3.364 0.656 4.000 4.000 4.000 0.9348453751 49 3.982 -3.364 0.656 3.787 4.000 4.000 0.9348366497 50 3.982 -3.364 0.656 3.892 4.000 4.000 0.9342836280 52 3.982 -3.364 0.656 3.886 4.000 4.000 0.9342795279 55 3.982 -3.364 0.656 3.880 4.000 4.000 0.9342790451 65 3.982 -3.364 0.656 3.879 4.382 4.000 0.9305000858 69 3.982 -3.364 0.656 3.879 4.357 4.000 0.9304589520 71 3.982 -3.364 0.656 3.879 4.361 4.000 0.9304563373 79 3.982 -3.364 0.656 3.879 4.361 3.382 0.9290458494 80 3.982 -3.364 0.656 3.879 4.361 3.000 0.9277553111 83 3.982 -3.364 0.656 3.879 4.361 3.055 0.9276603266 85 3.982 -3.364 0.656 3.879 4.361 3.053 0.9276601795 87 3.982 -3.364 0.656 3.879 4.361 3.046 0.9276601180 88 3.982 -3.364 0.656 3.879 4.361 3.049 0.9276600488 89 3.982 -3.364 0.656 3.879 4.361 3.048 0.9276597447 96 3.364 -3.364 0.656 3.879 4.361 3.048 0.9219256664 98 3.282 -3.364 0.656 3.879 4.361 3.048 0.9213976351 99 3.216 -3.364 0.656 3.879 4.361 3.048 0.9211646044 103 3.225 -3.364 0.656 3.879 4.361 3.048 0.9211601090 104 3.224 -3.364 0.656 3.879 4.361 3.048 0.9211598857 112 3.224 -3.199 0.656 3.879 4.361 3.048 0.9206971731 114 3.224 -3.116 0.656 3.879 4.361 3.048 0.9205876156 115 3.224 -3.147 0.656 3.879 4.361 3.048 0.9205413178 116 3.224 -3.145 0.656 3.879 4.361 3.048 0.9205407004 118 3.224 -3.144 0.656 3.879 4.361 3.048 0.9205402243 125 3.224 -3.144 0.667 3.879 4.361 3.048 0.9205090874 126 3.224 -3.144 0.715 3.879 4.361 3.048 0.9204713839 129 3.224 -3.144 0.718 3.879 4.361 3.048 0.9204701098 130 3.224 -3.144 0.764 3.879 4.361 3.048 0.9202312650 131 3.224 -3.144 0.792 3.879 4.361 3.048 0.9202291951 132 3.224 -3.144 0.779 3.879 4.361 3.048 0.9201830875 141 3.224 -3.144 0.779 4.033 4.361 3.048 0.9193203224 142 3.224 -3.144 0.779 4.045 4.361 3.048 0.9192701993 144 3.224 -3.144 0.779 4.074 4.361 3.048 0.9192028511 146 3.224 -3.144 0.779 4.075 4.361 3.048 0.9192016732 147 3.224 -3.144 0.779 4.077 4.361 3.048 0.9192002772 157 3.224 -3.144 0.779 4.077 4.125 3.048 0.9183307104 160 3.224 -3.144 0.779 4.077 4.161 3.048 0.9179017047 162 3.224 -3.144 0.779 4.077 4.164 3.048 0.9178791845 164 3.224 -3.144 0.779 4.077 4.171 3.048 0.9178486802 165 3.224 -3.144 0.779 4.077 4.172 3.048 0.9178479372 177 3.224 -3.144 0.779 4.077 4.172 3.026 0.9178054674 179 3.224 -3.144 0.779 4.077 4.172 3.030 0.9178037800 193 3.219 -3.144 0.779 4.077 4.172 3.031 0.9177978215 203 3.219 -3.150 0.779 4.077 4.172 3.031 0.9177892887 204 3.219 -3.157 0.779 4.077 4.172 3.031 0.9177878832 205 3.219 -3.155 0.779 4.077 4.172 3.031 0.9177876170 215 3.219 -3.155 0.787 4.077 4.172 3.031 0.9177803026 217 3.219 -3.155 0.788 4.077 4.172 3.031 0.9177802754 225 3.219 -3.155 0.788 4.054 4.172 3.031 0.9177670979 226 3.219 -3.155 0.788 4.056 4.172 3.031 0.9177620123 227 3.219 -3.155 0.788 4.064 4.172 3.031 0.9177543553 240 3.219 -3.155 0.788 4.064 4.173 3.031 0.9177468096 241 3.219 -3.155 0.788 4.064 4.179 3.031 0.9177273677 256 3.219 -3.155 0.788 4.064 4.179 3.023 0.9177257830 257 3.219 -3.155 0.788 4.064 4.179 3.026 0.9177239769 Powell done niters = 2 Computing relative cost 0 -25.0 -25.0 -25.0 1.039014 1 -25.0 -25.0 25.0 1.099395 2 -25.0 25.0 -25.0 1.077594 3 -25.0 25.0 25.0 1.047730 4 25.0 -25.0 -25.0 1.058904 5 25.0 -25.0 25.0 0.992387 6 25.0 25.0 -25.0 1.014665 7 25.0 25.0 25.0 1.047133 REL: 8 0.917724 8.376823 1.047103 rel = 0.876441 Number of iterations 2 Min cost was 0.917724 Number of FunctionCalls 260 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.478000 sec Parameters at optimum (transmm) 3.21927 -3.15482 0.78838 Parameters at optimum (rotdeg) 4.06387 4.17879 3.02591 Final costs ---------------- Number of surface hits 2593 WM Intensity 845.4333 +/- 217.3218 Ctx Intensity 839.5874 +/- 236.3597 Pct Contrast -2.2666 +/- 22.5927 Cost 0.9177 RelCost 0.9513 Reg at min cost was -0.996 -0.079 -0.051 3.558; -0.058 0.089 0.994 -5.296; 0.074 -0.993 0.093 11.078; 0.000 0.000 0.000 1.000; Writing optimal reg to bbregister/tmp.bbregister.822/bbr.pass1.dat, type = 14 Original Reg -1.000 -0.002 -0.006 -0.525; -0.006 0.022 1.000 -1.422; 0.001 -1.000 0.022 10.406; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.004 0.077 0.046 -4.083; 0.053 -0.067 0.005 3.874; -0.072 -0.007 -0.071 -0.672; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 6.954521 Computing change in rh position Surface RMS Diff (mm) 8.092520 15.279243 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 bbregister/tmp.bbregister.822/template.nii --init-reg bbregister/tmp.bbregister.822/bbr.pass1.dat --out-reg bbregister/fmri-TO-orig.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bbregister/fmri-TO-orig.dat.mincost --dof 6 --nmax 36 --param bbregister/fmri-TO-orig.dat.param --surf white --cur-reg bbregister/tmp.bbregister.822/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 /home/kayhan/test/myproject/control001/tp1 cd /home/kayhan/test/myproject/control001/tp1/NIFTI mri_segreg --mov bbregister/tmp.bbregister.822/template.nii --init-reg bbregister/tmp.bbregister.822/bbr.pass1.dat --out-reg bbregister/fmri-TO-orig.dat --brute -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bbregister/fmri-TO-orig.dat.mincost --dof 6 --nmax 36 --param bbregister/fmri-TO-orig.dat.param --surf white --cur-reg bbregister/tmp.bbregister.822/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname sbia-pc71 machine x86_64 user kayhan movvol bbregister/tmp.bbregister.822/template.nii regfile bbregister/tmp.bbregister.822/bbr.pass1.dat subject FREESURFER dof 6 outregfile bbregister/fmri-TO-orig.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 1333809888 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.996 -0.079 -0.051 3.558; -0.058 0.089 0.994 -5.296; 0.074 -0.993 0.093 11.078; 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 Computing relative cost 0 -25.0 -25.0 -25.0 1.056962 1 -25.0 -25.0 25.0 1.064207 2 -25.0 25.0 -25.0 1.045309 3 -25.0 25.0 25.0 1.052528 4 25.0 -25.0 -25.0 1.047138 5 25.0 -25.0 25.0 0.999516 6 25.0 25.0 -25.0 1.015514 7 25.0 25.0 25.0 1.049502 REL: 8 0.971065 8.330677 1.041335 rel = 0.93252 Initial costs ---------------- Number of surface hits 259591 WM Intensity 844.1337 +/- 217.7580 Ctx Intensity 834.1648 +/- 236.8957 Pct Contrast -2.8538 +/- 22.7195 Cost 0.9711 RelCost 0.9325 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 -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.9213 0.9213 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.9193 0.9193 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.9180 0.9180 0.0 48 -0.1000 -0.1000 0.0000 0.1000 0.0000 -0.1000 0.9179 0.9179 0.0 102 -0.1000 0.0000 -0.1000 0.1000 0.0000 -0.1000 0.9175 0.9175 0.0 129 -0.1000 0.0000 0.0000 0.1000 0.0000 -0.1000 0.9175 0.9175 0.0 282 0.0000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.9174 0.9174 0.0 Brute Force -------------------------- Min cost was 0.917383 Number of iterations 729 Search time 1.296000 sec Parameters at best (transmm, rotdeg) 0.000 -0.100 0.000 0.000 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 -0.1 2 0 3 0 4 0 5 -0.1 7 -0.188 -0.100 0.000 0.000 0.000 -0.100 0.9713561794 9 -0.185 -0.100 0.000 0.000 0.000 -0.100 0.9713554621 12 -0.165 -0.100 0.000 0.000 0.000 -0.100 0.9713553668 13 -0.175 -0.100 0.000 0.000 0.000 -0.100 0.9713540186 15 -0.174 -0.100 0.000 0.000 0.000 -0.100 0.9713539387 20 -0.172 0.900 0.000 0.000 0.000 -0.100 0.9658947215 26 -0.172 0.925 0.000 0.000 0.000 -0.100 0.9658826202 28 -0.172 0.922 0.000 0.000 0.000 -0.100 0.9658823108 30 -0.172 0.921 0.000 0.000 0.000 -0.100 0.9658822713 32 -0.172 0.920 0.000 0.000 0.000 -0.100 0.9658822424 35 -0.172 0.920 -1.618 0.000 0.000 -0.100 0.9628261795 36 -0.172 0.920 -0.982 0.000 0.000 -0.100 0.9619918756 40 -0.172 0.920 -1.057 0.000 0.000 -0.100 0.9619822644 41 -0.172 0.920 -1.047 0.000 0.000 -0.100 0.9619817350 42 -0.172 0.920 -1.043 0.000 0.000 -0.100 0.9619813005 44 -0.172 0.920 -1.034 0.000 0.000 -0.100 0.9619810246 45 -0.172 0.920 -1.035 0.000 0.000 -0.100 0.9619810190 46 -0.172 0.920 -1.036 0.000 0.000 -0.100 0.9619809948 47 -0.172 0.920 -1.039 0.000 0.000 -0.100 0.9619809771 54 -0.172 0.920 -1.038 -0.618 0.000 -0.100 0.9606596037 56 -0.172 0.920 -1.038 -0.705 0.000 -0.100 0.9605874691 58 -0.172 0.920 -1.038 -0.722 0.000 -0.100 0.9605843211 59 -0.172 0.920 -1.038 -0.723 0.000 -0.100 0.9605842249 61 -0.172 0.920 -1.038 -0.725 0.000 -0.100 0.9605841920 64 -0.172 0.920 -1.038 -0.725 1.000 -0.100 0.9531169825 69 -0.172 0.920 -1.038 -0.725 1.264 -0.100 0.9526023243 71 -0.172 0.920 -1.038 -0.725 1.240 -0.100 0.9525856325 73 -0.172 0.920 -1.038 -0.725 1.205 -0.100 0.9525610451 81 -0.172 0.920 -1.038 -0.725 1.205 0.900 0.9487911346 82 -0.172 0.920 -1.038 -0.725 1.205 2.518 0.9468823329 84 -0.172 0.920 -1.038 -0.725 1.205 5.136 0.9456226426 87 -0.172 0.920 -1.038 -0.725 1.205 4.136 0.9435671090 89 -0.172 0.920 -1.038 -0.725 1.205 4.262 0.9433974129 91 -0.172 0.920 -1.038 -0.725 1.205 4.378 0.9432871502 92 -0.172 0.920 -1.038 -0.725 1.205 4.398 0.9432829294 93 -0.172 0.920 -1.038 -0.725 1.205 4.407 0.9432789195 95 -0.172 0.920 -1.038 -0.725 1.205 4.435 0.9432718096 97 -0.172 0.920 -1.038 -0.725 1.205 4.428 0.9432709463 103 -1.790 0.920 -1.038 -0.725 1.205 4.428 0.9338297531 104 -1.433 0.920 -1.038 -0.725 1.205 4.428 0.9333012485 113 -1.428 0.920 -1.038 -0.725 1.205 4.428 0.9333007203 118 -1.429 1.920 -1.038 -0.725 1.205 4.428 0.9322953445 122 -1.429 1.538 -1.038 -0.725 1.205 4.428 0.9316123272 124 -1.429 1.564 -1.038 -0.725 1.205 4.428 0.9316070764 127 -1.429 1.560 -1.038 -0.725 1.205 4.428 0.9316067889 128 -1.429 1.556 -1.038 -0.725 1.205 4.428 0.9316066624 129 -1.429 1.557 -1.038 -0.725 1.205 4.428 0.9316065760 135 -1.429 1.558 -1.656 -0.725 1.205 4.428 0.9302069047 141 -1.429 1.558 -1.621 -0.725 1.205 4.428 0.9302067562 145 -1.429 1.558 -1.627 -0.725 1.205 4.428 0.9302067346 153 -1.429 1.558 -1.626 -2.343 1.205 4.428 0.9276599458 154 -1.429 1.558 -1.626 -1.919 1.205 4.428 0.9268283687 161 -1.429 1.558 -1.626 -1.893 1.205 4.428 0.9268237697 163 -1.429 1.558 -1.626 -1.897 1.205 4.428 0.9268229407 165 -1.429 1.558 -1.626 -1.901 1.205 4.428 0.9268229348 170 -1.429 1.558 -1.626 -1.904 2.205 4.428 0.9226125463 175 -1.429 1.558 -1.626 -1.904 2.178 4.428 0.9225988409 177 -1.429 1.558 -1.626 -1.904 2.170 4.428 0.9225972924 178 -1.429 1.558 -1.626 -1.904 2.169 4.428 0.9225972493 179 -1.429 1.558 -1.626 -1.904 2.168 4.428 0.9225971630 187 -1.429 1.558 -1.626 -1.904 2.166 3.810 0.9212042400 195 -1.429 1.558 -1.626 -1.904 2.166 3.813 0.9212042153 198 -1.429 1.558 -1.626 -1.904 2.166 3.815 0.9212042092 207 -1.614 1.558 -1.626 -1.904 2.166 3.814 0.9208748941 208 -1.622 1.558 -1.626 -1.904 2.166 3.814 0.9208737975 209 -1.626 1.558 -1.626 -1.904 2.166 3.814 0.9208729533 213 -1.636 1.558 -1.626 -1.904 2.166 3.814 0.9208712707 220 -1.637 0.940 -1.626 -1.904 2.166 3.814 0.9191270355 223 -1.637 0.988 -1.626 -1.904 2.166 3.814 0.9191155021 224 -1.637 0.986 -1.626 -1.904 2.166 3.814 0.9191153088 226 -1.637 0.984 -1.626 -1.904 2.166 3.814 0.9191152883 233 -1.637 0.983 -1.244 -1.904 2.166 3.814 0.9189643239 234 -1.637 0.983 -1.382 -1.904 2.166 3.814 0.9188512634 236 -1.637 0.983 -1.373 -1.904 2.166 3.814 0.9188505114 237 -1.637 0.983 -1.371 -1.904 2.166 3.814 0.9188504018 240 -1.637 0.983 -1.370 -1.904 2.166 3.814 0.9188503557 242 -1.637 0.983 -1.369 -1.904 2.166 3.814 0.9188503277 250 -1.637 0.983 -1.369 -2.111 2.166 3.814 0.9185948492 253 -1.637 0.983 -1.369 -2.101 2.166 3.814 0.9185929588 262 -1.637 0.983 -1.369 -2.101 2.186 3.814 0.9185427220 263 -1.637 0.983 -1.369 -2.101 2.261 3.814 0.9185029987 265 -1.637 0.983 -1.369 -2.101 2.237 3.814 0.9184913536 277 -1.637 0.983 -1.369 -2.101 2.235 3.760 0.9184757612 279 -1.637 0.983 -1.369 -2.101 2.235 3.772 0.9184729270 281 -1.637 0.983 -1.369 -2.101 2.235 3.779 0.9184724154 282 -1.637 0.983 -1.369 -2.101 2.235 3.780 0.9184723411 285 -1.637 0.983 -1.369 -2.101 2.235 3.782 0.9184723363 295 -1.640 0.983 -1.369 -2.101 2.235 3.782 0.9184719806 305 -1.640 1.017 -1.369 -2.101 2.235 3.782 0.9184632323 308 -1.640 1.016 -1.369 -2.101 2.235 3.782 0.9184631547 317 -1.640 1.015 -1.333 -2.101 2.235 3.782 0.9184582715 318 -1.640 1.015 -1.335 -2.101 2.235 3.782 0.9184580111 319 -1.640 1.015 -1.342 -2.101 2.235 3.782 0.9184574789 320 -1.640 1.015 -1.352 -2.101 2.235 3.782 0.9184574666 321 -1.640 1.015 -1.348 -2.101 2.235 3.782 0.9184572000 323 -1.640 1.015 -1.349 -2.101 2.235 3.782 0.9184571906 331 -1.640 1.015 -1.349 -2.136 2.235 3.782 0.9184569334 332 -1.640 1.015 -1.349 -2.119 2.235 3.782 0.9184512500 343 -1.640 1.015 -1.349 -2.118 2.246 3.782 0.9184496752 353 -1.640 1.015 -1.349 -2.118 2.245 3.753 0.9184439393 354 -1.640 1.015 -1.349 -2.118 2.245 3.754 0.9184437306 355 -1.640 1.015 -1.349 -2.118 2.245 3.760 0.9184423941 357 -1.640 1.015 -1.349 -2.118 2.245 3.762 0.9184423333 368 -1.648 1.015 -1.349 -2.118 2.245 3.762 0.9184409282 369 -1.650 1.015 -1.349 -2.118 2.245 3.762 0.9184407491 370 -1.652 1.015 -1.349 -2.118 2.245 3.762 0.9184406555 374 -1.654 1.015 -1.349 -2.118 2.245 3.762 0.9184406497 382 -1.654 1.003 -1.349 -2.118 2.245 3.762 0.9184406121 383 -1.654 1.009 -1.349 -2.118 2.245 3.762 0.9184400004 387 -1.654 1.010 -1.349 -2.118 2.245 3.762 0.9184399948 395 -1.654 1.010 -1.336 -2.118 2.245 3.762 0.9184392733 397 -1.654 1.010 -1.340 -2.118 2.245 3.762 0.9184391561 399 -1.654 1.010 -1.339 -2.118 2.245 3.762 0.9184391545 400 -1.654 1.010 -1.338 -2.118 2.245 3.762 0.9184391443 409 -1.654 1.010 -1.338 -2.126 2.245 3.762 0.9184371081 410 -1.654 1.010 -1.338 -2.128 2.245 3.762 0.9184369622 421 -1.654 1.010 -1.338 -2.128 2.257 3.762 0.9184355483 422 -1.654 1.010 -1.338 -2.128 2.254 3.762 0.9184353929 433 -1.654 1.010 -1.338 -2.128 2.254 3.759 0.9184353027 436 -1.667 1.006 -1.328 -2.138 2.264 3.756 0.9184316645 439 -1.688 0.999 -1.311 -2.153 2.280 3.752 0.9184306485 448 -1.689 0.999 -1.310 -2.154 2.280 3.752 0.9184305809 450 -1.689 0.999 -1.310 -2.154 2.280 3.752 0.9184305801 452 -1.689 0.999 -1.310 -2.154 2.280 3.752 0.9184305077 467 -1.691 0.999 -1.310 -2.154 2.280 3.752 0.9184304063 476 -1.691 0.936 -1.310 -2.154 2.280 3.752 0.9184268633 477 -1.691 0.964 -1.310 -2.154 2.280 3.752 0.9184153341 478 -1.691 0.965 -1.310 -2.154 2.280 3.752 0.9184151179 480 -1.691 0.968 -1.310 -2.154 2.280 3.752 0.9184150147 488 -1.691 0.967 -1.287 -2.154 2.280 3.752 0.9184145421 489 -1.691 0.967 -1.296 -2.154 2.280 3.752 0.9184144447 502 -1.691 0.967 -1.288 -2.154 2.280 3.694 0.9183979158 504 -1.691 0.967 -1.288 -2.154 2.280 3.687 0.9183977856 506 -1.691 0.967 -1.288 -2.154 2.280 3.682 0.9183976433 507 -1.691 0.967 -1.288 -2.154 2.280 3.676 0.9183970285 521 -1.691 0.967 -1.288 -2.154 2.284 3.676 0.9183968450 523 -1.691 0.967 -1.288 -2.154 2.283 3.676 0.9183968363 524 -1.691 0.967 -1.288 -2.154 2.282 3.676 0.9183968200 526 -1.705 0.962 -1.277 -2.164 2.291 3.674 0.9183777246 527 -1.726 0.955 -1.260 -2.179 2.307 3.669 0.9183468935 532 -1.774 0.939 -1.223 -2.214 2.342 3.660 0.9183142832 534 -1.758 0.944 -1.235 -2.202 2.330 3.663 0.9183065220 536 -1.761 0.943 -1.233 -2.205 2.333 3.662 0.9183056217 554 -1.747 0.943 -1.233 -2.205 2.333 3.662 0.9182997528 563 -1.747 0.908 -1.233 -2.205 2.333 3.662 0.9182955922 564 -1.747 0.918 -1.233 -2.205 2.333 3.662 0.9182933470 565 -1.747 0.921 -1.233 -2.205 2.333 3.662 0.9182929459 566 -1.747 0.930 -1.233 -2.205 2.333 3.662 0.9182926078 570 -1.747 0.929 -1.233 -2.205 2.333 3.662 0.9182926035 577 -1.747 0.929 -1.223 -2.205 2.333 3.662 0.9182903062 579 -1.747 0.929 -1.215 -2.205 2.333 3.662 0.9182900223 580 -1.747 0.929 -1.217 -2.205 2.333 3.662 0.9182899355 602 -1.747 0.929 -1.218 -2.205 2.335 3.662 0.9182895951 610 -1.752 0.927 -1.214 -2.208 2.340 3.661 0.9182882955 611 -1.753 0.927 -1.214 -2.209 2.341 3.661 0.9182882610 615 -1.753 0.927 -1.214 -2.209 2.341 3.661 0.9182882404 628 -1.748 0.927 -1.214 -2.209 2.341 3.661 0.9182879864 641 -1.747 0.922 -1.214 -2.209 2.341 3.661 0.9182876948 664 -1.747 0.921 -1.213 -2.209 2.341 3.665 0.9182873389 666 -1.747 0.921 -1.213 -2.209 2.341 3.664 0.9182873290 676 -1.747 0.921 -1.213 -2.209 2.334 3.664 0.9182862556 685 -1.752 0.919 -1.209 -2.212 2.339 3.663 0.9182857491 689 -1.752 0.919 -1.209 -2.212 2.339 3.663 0.9182857227 698 -1.750 0.912 -1.204 -2.216 2.338 3.666 0.9182839806 701 -1.749 0.900 -1.197 -2.221 2.335 3.669 0.9182834386 725 -1.735 0.900 -1.197 -2.221 2.335 3.669 0.9182793789 737 -1.735 0.903 -1.197 -2.221 2.335 3.669 0.9182790806 738 -1.735 0.904 -1.197 -2.221 2.335 3.669 0.9182789976 739 -1.735 0.907 -1.197 -2.221 2.335 3.669 0.9182787530 750 -1.735 0.907 -1.201 -2.221 2.335 3.669 0.9182785471 753 -1.735 0.907 -1.202 -2.221 2.335 3.669 0.9182784836 754 -1.735 0.907 -1.203 -2.221 2.335 3.669 0.9182784653 775 -1.736 0.906 -1.203 -2.222 2.336 3.667 0.9182783997 779 -1.735 0.899 -1.198 -2.225 2.335 3.669 0.9182769838 780 -1.734 0.887 -1.190 -2.231 2.332 3.673 0.9182765910 781 -1.734 0.891 -1.193 -2.229 2.333 3.672 0.9182762181 803 -1.731 0.891 -1.193 -2.229 2.333 3.672 0.9182762025 805 -1.732 0.891 -1.193 -2.229 2.333 3.672 0.9182761409 815 -1.733 0.898 -1.193 -2.229 2.333 3.672 0.9182759203 816 -1.733 0.895 -1.193 -2.229 2.333 3.672 0.9182753894 817 -1.733 0.894 -1.193 -2.229 2.333 3.672 0.9182753580 836 -1.733 0.894 -1.194 -2.229 2.333 3.668 0.9182752533 837 -1.733 0.894 -1.194 -2.229 2.333 3.667 0.9182752360 860 -1.732 0.887 -1.189 -2.232 2.332 3.668 0.9182751693 864 -1.733 0.890 -1.191 -2.231 2.332 3.667 0.9182750334 866 -1.733 0.890 -1.191 -2.231 2.332 3.667 0.9182750216 869 -1.733 0.890 -1.191 -2.231 2.332 3.667 0.9182750208 870 -1.731 0.888 -1.189 -2.234 2.332 3.663 0.9182740667 873 -1.729 0.886 -1.185 -2.237 2.330 3.657 0.9182736981 874 -1.730 0.886 -1.186 -2.236 2.331 3.658 0.9182736104 878 -1.730 0.887 -1.187 -2.236 2.331 3.659 0.9182735560 896 -1.725 0.887 -1.187 -2.236 2.331 3.659 0.9182732815 897 -1.726 0.887 -1.187 -2.236 2.331 3.659 0.9182732294 905 -1.726 0.886 -1.186 -2.236 2.331 3.659 0.9182732092 908 -1.726 0.886 -1.186 -2.236 2.331 3.660 0.9182731792 913 -1.726 0.886 -1.186 -2.236 2.331 3.660 0.9182731542 916 -1.726 0.886 -1.186 -2.236 2.331 3.660 0.9182731455 925 -1.726 0.886 -1.188 -2.236 2.331 3.660 0.9182730358 926 -1.726 0.886 -1.191 -2.236 2.331 3.660 0.9182729864 930 -1.726 0.886 -1.193 -2.236 2.331 3.660 0.9182729691 959 -1.725 0.884 -1.192 -2.239 2.330 3.655 0.9182729252 963 -1.725 0.885 -1.193 -2.238 2.330 3.657 0.9182729161 964 -1.725 0.884 -1.193 -2.238 2.330 3.656 0.9182728387 969 -1.725 0.884 -1.193 -2.238 2.330 3.656 0.9182728341 984 -1.726 0.884 -1.193 -2.238 2.330 3.656 0.9182728097 997 -1.726 0.884 -1.193 -2.238 2.330 3.656 0.9182727688 1023 -1.726 0.884 -1.192 -2.238 2.330 3.662 0.9182727295 1024 -1.726 0.884 -1.192 -2.238 2.330 3.659 0.9182725937 1026 -1.726 0.884 -1.192 -2.238 2.330 3.660 0.9182725721 1056 -1.726 0.884 -1.192 -2.238 2.330 3.660 0.9182725197 1070 -1.728 0.884 -1.192 -2.238 2.330 3.660 0.9182725009 1099 -1.728 0.884 -1.193 -2.238 2.330 3.661 0.9182724777 1131 -1.726 0.882 -1.192 -2.241 2.329 3.656 0.9182724189 1140 -1.726 0.883 -1.192 -2.241 2.329 3.657 0.9182723978 1145 -1.726 0.883 -1.192 -2.241 2.329 3.656 0.9182723562 1166 -1.725 0.881 -1.191 -2.241 2.329 3.657 0.9182722832 1190 -1.725 0.881 -1.191 -2.241 2.329 3.659 0.9182721645 1201 -1.725 0.881 -1.192 -2.241 2.329 3.659 0.9182721335 1203 -1.725 0.881 -1.191 -2.241 2.329 3.659 0.9182721331 1205 -1.725 0.881 -1.191 -2.241 2.329 3.659 0.9182720710 1242 -1.726 0.881 -1.191 -2.241 2.329 3.659 0.9182720549 1265 -1.726 0.881 -1.192 -2.241 2.329 3.662 0.9182720028 1284 -1.726 0.881 -1.193 -2.240 2.328 3.662 0.9182719934 1285 -1.726 0.881 -1.193 -2.240 2.328 3.662 0.9182719120 1288 -1.724 0.880 -1.191 -2.243 2.327 3.658 0.9182718948 1293 -1.724 0.880 -1.191 -2.243 2.328 3.658 0.9182718762 1297 -1.724 0.880 -1.191 -2.243 2.328 3.658 0.9182718189 1330 -1.724 0.880 -1.191 -2.243 2.328 3.658 0.9182718180 1366 -1.723 0.880 -1.191 -2.242 2.327 3.660 0.9182717912 1367 -1.723 0.880 -1.191 -2.242 2.327 3.660 0.9182717627 1368 -1.723 0.880 -1.191 -2.242 2.327 3.660 0.9182717018 1417 -1.724 0.880 -1.190 -2.242 2.326 3.659 0.9182716878 1454 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182716839 1469 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182716398 1470 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182716173 1471 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182715794 1517 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182715733 1525 -1.724 0.880 -1.189 -2.242 2.326 3.660 0.9182715713 1571 -1.724 0.880 -1.189 -2.242 2.326 3.660 0.9182715629 1572 -1.724 0.880 -1.189 -2.242 2.326 3.660 0.9182715559 1647 -1.724 0.880 -1.190 -2.242 2.326 3.660 0.9182715520 Powell done niters = 18 Computing relative cost 0 -25.0 -25.0 -25.0 1.056434 1 -25.0 -25.0 25.0 1.057838 2 -25.0 25.0 -25.0 1.053712 3 -25.0 25.0 25.0 1.042529 4 25.0 -25.0 -25.0 1.040193 5 25.0 -25.0 25.0 1.004880 6 25.0 25.0 -25.0 0.994241 7 25.0 25.0 25.0 1.052396 REL: 8 0.918272 8.302222 1.037778 rel = 0.884844 Number of iterations 18 Min cost was 0.918272 Number of FunctionCalls 1651 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 120.995000 sec Parameters at optimum (transmm) -1.72361 0.88006 -1.19036 Parameters at optimum (rotdeg) -2.24224 2.32639 3.66023 Final costs ---------------- Number of surface hits 259591 WM Intensity 861.5031 +/- 199.6492 Ctx Intensity 854.6360 +/- 220.0934 Pct Contrast -2.3483 +/- 21.2328 Cost 0.9183 RelCost 0.9325 Reg at min cost was -0.986 -0.122 -0.113 2.591; -0.119 0.042 0.992 -3.712; 0.116 -0.992 0.056 9.933; 0.000 0.000 0.000 1.000; Writing optimal reg to bbregister/fmri-TO-orig.dat, type = 14 Original Reg -0.996 -0.079 -0.051 3.558; -0.058 0.089 0.994 -5.296; 0.074 -0.993 0.093 11.078; 0.000 0.000 0.000 1.000; Original Reg - Optimal Reg -0.009 0.043 0.061 0.967; 0.060 0.047 0.002 -1.584; -0.043 -0.001 0.037 1.145; 0.000 0.000 0.000 0.000; Computing change in lh position LH rmsDiffMean 5.539707 Computing change in rh position Surface RMS Diff (mm) 4.231588 8.512540 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 tkregister2_cmdl --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat --noedit --fslregout bbregister/fmri-TO-orig.mat tkregister_tcl /opt/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume fMRI.nii.gz reg file bbregister/fmri-TO-orig.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.986 -0.122 -0.113 2.591; -0.119 0.042 0.992 -3.712; 0.116 -0.992 0.056 9.933; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /home/kayhan/test/myproject/control001/tp1/FREESURFER/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 fMRI.nii.gz Tmov: -------------------- -3.125 0.000 0.000 100.000; 0.000 0.000 4.200 -69.300; 0.000 -3.125 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.986 -0.122 -0.113 2.591; -0.119 0.042 0.992 -3.712; 0.116 -0.992 0.056 9.933; 0.000 0.000 0.000 1.000; Determinant -1 subject = FREESURFER RegMat --------------------------- -0.986 -0.122 -0.113 2.591; -0.119 0.042 0.992 -3.712; 0.116 -0.992 0.056 9.933; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI_GZ tkreg2FSL: mov det = -41.0156, ref det = -1 Cleaning up Started at Sun Apr 1 20:44:56 EDT 2012 Ended at Sun Apr 1 20:47:39 EDT 2012 BBR-Run-Time-Sec 163 bbregister Done To check results, run: tkregister2 --mov fMRI.nii.gz --reg bbregister/fmri-TO-orig.dat --surf