Logfile for bbregister Wed Jul 12 17:31:55 EDT 2023 setenv SUBJECTS_DIR /autofs/space/nyx_002/users/edann/test_tutorial/fs cd /autofs/space/nyx_002/users/edann/test_tutorial /usr/local/freesurfer/7.3.2/bin/bbregister --s sub-BANDA001 --init-fsl --dti --6 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.lta bbregister 7.3.2 Linux curie.nmr.mgh.harvard.edu 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/7.3.2 mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii reading from /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999223, 0.0236447, -0.0315337) j_ras = (0.0113363, 0.938674, 0.344621) k_ras = (-0.0377483, -0.343995, 0.938212) writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii... fslregister --s sub-BANDA001 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --niters 1 --maxangle 90 --tmp /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat.fslregister.log Wed Jul 12 17:31:55 EDT 2023 --s sub-BANDA001 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --niters 1 --maxangle 90 --tmp /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov fslregister 7.3.2 curie.nmr.mgh.harvard.edu Linux curie.nmr.mgh.harvard.edu 3.10.0-1160.92.1.el7.x86_64 #1 SMP Tue Jun 20 11:48:01 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /autofs/space/nyx_002/users/edann/test_tutorial mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/brainmask.mgz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/refvol.fslregister.nii mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/brainmask.mgz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/refvol.fslregister.nii reading from /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/brainmask.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1.16415e-10, -1) k_ras = (0, 1, -5.82077e-11) writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/refvol.fslregister.nii... -------------------------------------- /autofs/space/nyx_002/users/edann/test_tutorial mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii --frame 0 reading from /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999223, 0.0236447, -0.0315337) j_ras = (0.0113363, 0.938674, 0.344621) k_ras = (-0.0377483, -0.343995, 0.938212) keeping frame 0 writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii... Mov determinant is -3.375 /autofs/space/nyx_002/users/edann/test_tutorial tkregister2_cmdl --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/reg0.172749.dat --targ brainmask --fstarg --regheader --fslregout /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat.fsl.mat0 --s sub-BANDA001 --noedit target volume brainmask movable volume /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/reg0.172749.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 INFO: loading target /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/brainmask.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.50000 0.00000 0.00000 105.00000; 0.00000 0.00000 1.50000 -69.00000; 0.00000 -1.50000 0.00000 105.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.99922 -0.02364 0.03153 -0.40044; -0.03775 -0.34400 0.93821 -34.65819; -0.01134 -0.93867 -0.34462 -10.80309; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99922 -0.02364 0.03153 -0.40044; -0.03775 -0.34400 0.93821 -34.65819; -0.01134 -0.93867 -0.34462 -10.80309; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-BANDA001 RegMat --------------------------- 0.99922 -0.02364 0.03153 -0.40044; -0.03775 -0.34400 0.93821 -34.65819; -0.01134 -0.93867 -0.34462 -10.80309; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -3.375, ref det = -1 Wed Jul 12 17:31:56 EDT 2023 /autofs/space/nyx_002/users/edann/test_tutorial flirt.fsl -ref /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/refvol.fslregister.nii -in /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/7.3.2/bin/fsl.5.0.2.xyztrans.sch -init /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat.fsl.mat0 Wed Jul 12 17:32:04 EDT 2023 /autofs/space/nyx_002/users/edann/test_tutorial flirt.fsl -ref /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/refvol.fslregister.nii -in /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat.fsl.mat -init /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/7.3.2/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub-BANDA001 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --targ brainmask --fstarg --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --fslreg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.99838 -0.01340 0.05526 21.96880; 0.04619 -0.37547 -0.92568 197.67000; 0.03315 0.92674 -0.37424 30.13210; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brainmask movable volume /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 INFO: loading target /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/brainmask.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii Tmov: -------------------- -1.50000 0.00000 0.00000 105.00000; 0.00000 0.00000 1.50000 -69.00000; 0.00000 -1.50000 0.00000 105.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -3.375, ref det = -1 ---- Input registration matrix (computed) -------- 0.99838 -0.03315 0.04619 -0.88622; -0.05526 -0.37424 0.92568 -35.27473; -0.01340 -0.92674 -0.37547 -10.43552; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99838 -0.03315 0.04619 -0.88622; -0.05526 -0.37424 0.92568 -35.27473; -0.01340 -0.92674 -0.37547 -10.43552; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-BANDA001 RegMat --------------------------- 0.99838 -0.03315 0.04619 -0.88622; -0.05526 -0.37424 0.92568 -35.27473; -0.01340 -0.92674 -0.37547 -10.43552; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: N (standard_in) 1: syntax error Started at Wed Jul 12 17:31:55 EDT 2023 Ended at Wed Jul 12 17:32:18 EDT 2023 fslregister Done To check results, run: tkregisterfv --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --surf orig mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/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 7.3.2 setenv SUBJECTS_DIR /autofs/space/nyx_002/users/edann/test_tutorial/fs cd /autofs/space/nyx_002/users/edann/test_tutorial mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/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 curie.nmr.mgh.harvard.edu machine x86_64 user cy281 movvol /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii regfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.init.dat subject sub-BANDA001 dof 6 outregfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/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 1689919099 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99838 -0.03315 0.04619 -0.88622; -0.05526 -0.37424 0.92568 -35.27473; -0.01340 -0.92674 -0.37547 -10.43552; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/orig.mgz 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 for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.980762 1 -25.0 -25.0 25.0 0.970191 2 -25.0 25.0 -25.0 0.987668 3 -25.0 25.0 25.0 0.962302 4 25.0 -25.0 -25.0 0.938215 5 25.0 -25.0 25.0 0.957961 6 25.0 25.0 -25.0 0.954069 7 25.0 25.0 25.0 0.989181 REL: 8 0.240661 7.740349 0.967544 rel = 0.248734 Initial costs ---------------- Number of surface hits 2766 WM Intensity 5205.5431 +/- 1636.1933 Ctx Intensity 6289.6855 +/- 1749.2032 Pct Contrast 19.5256 +/- 18.6279 Cost 0.2407 RelCost 0.2487 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9515 0.9515 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9487 0.9487 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9158 0.9158 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8479 0.8479 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8342 0.8342 0.0 46 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.0000 0.7701 0.7701 0.0 254 0.0000 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.7635 0.7635 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7108 0.7108 0.0 282 0.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.6997 0.6997 0.0 283 0.0000 -4.0000 0.0000 0.0000 0.0000 0.0000 0.6606 0.6606 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.5747 0.5747 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2407 0.2407 0.0 Brute Force -------------------------- Min cost was 0.240661 Number of iterations 729 Search time 1.051734 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.240661 7 -0.041 0.000 0.000 0.000 0.000 0.000 0.2403778704 8 -0.057 0.000 0.000 0.000 0.000 0.000 0.2401698456 10 -0.139 0.000 0.000 0.000 0.000 0.000 0.2395636057 12 -0.125 0.000 0.000 0.000 0.000 0.000 0.2395459420 13 -0.128 0.000 0.000 0.000 0.000 0.000 0.2395457109 15 -0.127 0.000 0.000 0.000 0.000 0.000 0.2395456085 18 -0.127 -1.618 0.000 0.000 0.000 0.000 0.1754713386 19 -0.127 -1.114 0.000 0.000 0.000 0.000 0.1501167762 23 -0.127 -1.102 0.000 0.000 0.000 0.000 0.1500610764 24 -0.127 -1.066 0.000 0.000 0.000 0.000 0.1496924328 26 -0.127 -1.011 0.000 0.000 0.000 0.000 0.1488231526 28 -0.127 -0.995 0.000 0.000 0.000 0.000 0.1487775445 30 -0.127 -0.988 0.000 0.000 0.000 0.000 0.1487743843 31 -0.127 -0.991 0.000 0.000 0.000 0.000 0.1487720263 39 -0.127 -0.991 0.382 0.000 0.000 0.000 0.1472231233 40 -0.127 -0.991 0.211 0.000 0.000 0.000 0.1446634385 41 -0.127 -0.991 0.213 0.000 0.000 0.000 0.1446566159 42 -0.127 -0.991 0.227 0.000 0.000 0.000 0.1446147978 44 -0.127 -0.991 0.249 0.000 0.000 0.000 0.1445944434 45 -0.127 -0.991 0.245 0.000 0.000 0.000 0.1445939158 46 -0.127 -0.991 0.246 0.000 0.000 0.000 0.1445938420 49 -0.127 -0.991 0.246 1.000 0.000 0.000 0.1338384768 53 -0.127 -0.991 0.246 0.618 0.000 0.000 0.1168358204 54 -0.127 -0.991 0.246 0.499 0.000 0.000 0.1162021698 57 -0.127 -0.991 0.246 0.495 0.000 0.000 0.1162013181 66 -0.127 -0.991 0.246 0.495 0.115 0.000 0.1147554906 69 -0.127 -0.991 0.246 0.495 0.116 0.000 0.1147553076 79 -0.127 -0.991 0.246 0.495 0.116 -0.040 0.1146860755 80 -0.127 -0.991 0.246 0.495 0.116 -0.039 0.1146848116 81 -0.127 -0.991 0.246 0.495 0.116 -0.031 0.1146811263 83 -0.127 -0.991 0.246 0.495 0.116 -0.032 0.1146810269 powell nthiter 1: fret = 0.114681 92 -0.034 -0.991 0.246 0.495 0.116 -0.032 0.1142057240 93 -0.053 -0.991 0.246 0.495 0.116 -0.032 0.1141179428 94 -0.061 -0.991 0.246 0.495 0.116 -0.032 0.1141116856 104 -0.061 -0.990 0.246 0.495 0.116 -0.032 0.1141115484 112 -0.061 -0.990 0.221 0.495 0.116 -0.032 0.1139772150 113 -0.061 -0.990 0.199 0.495 0.116 -0.032 0.1138822234 116 -0.061 -0.990 0.153 0.495 0.116 -0.032 0.1137849594 118 -0.061 -0.990 0.163 0.495 0.116 -0.032 0.1137776773 119 -0.061 -0.990 0.162 0.495 0.116 -0.032 0.1137773864 120 -0.061 -0.990 0.161 0.495 0.116 -0.032 0.1137772954 128 -0.061 -0.990 0.161 0.545 0.116 -0.032 0.1132249637 129 -0.061 -0.990 0.161 0.568 0.116 -0.032 0.1131139751 130 -0.061 -0.990 0.161 0.586 0.116 -0.032 0.1131054439 131 -0.061 -0.990 0.161 0.579 0.116 -0.032 0.1131012543 132 -0.061 -0.990 0.161 0.580 0.116 -0.032 0.1131008629 142 -0.061 -0.990 0.161 0.580 0.121 -0.032 0.1130975955 143 -0.061 -0.990 0.161 0.580 0.120 -0.032 0.1130975644 151 -0.061 -0.990 0.161 0.580 0.120 -0.196 0.1126103996 155 -0.061 -0.990 0.161 0.580 0.120 -0.253 0.1122667823 156 -0.061 -0.990 0.161 0.580 0.120 -0.257 0.1122648273 157 -0.061 -0.990 0.161 0.580 0.120 -0.258 0.1122637108 160 -0.061 -0.990 0.161 0.580 0.120 -0.262 0.1122620483 162 -0.061 -0.990 0.161 0.580 0.120 -0.261 0.1122619366 powell nthiter 2: fret = 0.112262 171 -0.029 -0.990 0.161 0.580 0.120 -0.261 0.1114668092 172 0.027 -0.990 0.161 0.580 0.120 -0.261 0.1111941255 175 0.018 -0.990 0.161 0.580 0.120 -0.261 0.1111871415 176 0.019 -0.990 0.161 0.580 0.120 -0.261 0.1111869783 177 0.020 -0.990 0.161 0.580 0.120 -0.261 0.1111869743 187 0.020 -0.969 0.161 0.580 0.120 -0.261 0.1111704554 189 0.020 -0.977 0.161 0.580 0.120 -0.261 0.1111580882 191 0.020 -0.978 0.161 0.580 0.120 -0.261 0.1111580430 200 0.020 -0.978 0.227 0.580 0.120 -0.261 0.1110466412 201 0.020 -0.978 0.206 0.580 0.120 -0.261 0.1109850849 202 0.020 -0.978 0.202 0.580 0.120 -0.261 0.1109825056 203 0.020 -0.978 0.200 0.580 0.120 -0.261 0.1109818108 206 0.020 -0.978 0.199 0.580 0.120 -0.261 0.1109817508 215 0.020 -0.978 0.199 0.631 0.120 -0.261 0.1107572143 217 0.020 -0.978 0.199 0.620 0.120 -0.261 0.1107381698 218 0.020 -0.978 0.199 0.619 0.120 -0.261 0.1107379453 226 0.020 -0.978 0.199 0.619 0.052 -0.261 0.1107071263 227 0.020 -0.978 0.199 0.619 0.084 -0.261 0.1104228506 229 0.020 -0.978 0.199 0.619 0.083 -0.261 0.1104227765 242 0.020 -0.978 0.199 0.619 0.083 -0.267 0.1104179976 powell nthiter 3: fret = 0.110418 253 0.041 -0.978 0.199 0.619 0.083 -0.267 0.1104110431 254 0.031 -0.978 0.199 0.619 0.083 -0.267 0.1103983031 255 0.032 -0.978 0.199 0.619 0.083 -0.267 0.1103979516 256 0.033 -0.978 0.199 0.619 0.083 -0.267 0.1103967514 258 0.034 -0.978 0.199 0.619 0.083 -0.267 0.1103961434 266 0.034 -0.983 0.199 0.619 0.083 -0.267 0.1103926543 276 0.034 -0.983 0.209 0.619 0.083 -0.267 0.1103824824 277 0.034 -0.983 0.210 0.619 0.083 -0.267 0.1103824440 286 0.034 -0.983 0.210 0.601 0.083 -0.267 0.1103422572 288 0.034 -0.983 0.210 0.602 0.083 -0.267 0.1103421824 301 0.034 -0.983 0.210 0.602 0.082 -0.267 0.1103419201 311 0.034 -0.983 0.210 0.602 0.082 -0.280 0.1103346714 312 0.034 -0.983 0.210 0.602 0.082 -0.275 0.1103329897 313 0.034 -0.983 0.210 0.602 0.082 -0.276 0.1103328690 powell nthiter 4: fret = 0.110333 325 0.033 -0.983 0.210 0.602 0.082 -0.276 0.1103326890 336 0.033 -0.981 0.210 0.602 0.082 -0.276 0.1103315993 347 0.033 -0.981 0.212 0.602 0.082 -0.276 0.1103313933 357 0.033 -0.981 0.212 0.601 0.082 -0.276 0.1103304349 358 0.033 -0.981 0.212 0.598 0.082 -0.276 0.1103287841 371 0.033 -0.981 0.212 0.598 0.077 -0.276 0.1103212071 383 0.033 -0.981 0.212 0.598 0.077 -0.280 0.1103208516 384 0.033 -0.981 0.212 0.598 0.077 -0.279 0.1103206119 powell nthiter 5: fret = 0.110321 395 0.034 -0.981 0.212 0.598 0.077 -0.279 0.1103201527 405 0.034 -0.982 0.212 0.598 0.077 -0.279 0.1103195410 415 0.034 -0.982 0.214 0.598 0.077 -0.279 0.1103191727 424 0.034 -0.982 0.214 0.594 0.077 -0.279 0.1103155769 425 0.034 -0.982 0.214 0.592 0.077 -0.279 0.1103155257 427 0.034 -0.982 0.214 0.593 0.077 -0.279 0.1103154058 436 0.034 -0.982 0.214 0.593 0.074 -0.279 0.1103147765 438 0.034 -0.982 0.214 0.593 0.075 -0.279 0.1103145825 449 0.034 -0.982 0.214 0.593 0.075 -0.280 0.1103143365 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.971812 1 -25.0 -25.0 25.0 0.968981 2 -25.0 25.0 -25.0 0.978447 3 -25.0 25.0 25.0 0.966580 4 25.0 -25.0 -25.0 0.952815 5 25.0 -25.0 25.0 0.961669 6 25.0 25.0 -25.0 0.955033 7 25.0 25.0 25.0 0.992522 REL: 8 0.110314 7.747860 0.968482 rel = 0.113904 Number of iterations 5 Min cost was 0.110314 Number of FunctionCalls 451 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.669758 sec Parameters at optimum (transmm) 0.03444 -0.98232 0.21360 Parameters at optimum (rotdeg) 0.59301 0.07530 -0.27958 Final costs ---------------- Number of surface hits 2766 WM Intensity 5090.5549 +/- 1565.4925 Ctx Intensity 6294.7578 +/- 1709.6565 Pct Contrast 21.7739 +/- 17.1686 Cost 0.1103 RelCost 0.2487 Reg at min cost was 0.99808 -0.03616 0.05025 -1.03755; -0.05999 -0.36446 0.92929 -36.14234; -0.01529 -0.93052 -0.36593 -10.58528; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/bbr.pass1.dat, type = 14 Original Reg 0.99838 -0.03315 0.04619 -0.88622; -0.05526 -0.37424 0.92568 -35.27473; -0.01340 -0.92674 -0.37547 -10.43552; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00030 0.00300 -0.00405 0.15133; 0.00473 -0.00978 -0.00360 0.86761; 0.00188 0.00378 -0.00954 0.14976; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.976274 Computing change in rh position Surface-RMS-Diff-mm 1.083035 0.421375 1.928811 mri_segreg done mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/bbr.pass1.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 7.3.2 setenv SUBJECTS_DIR /autofs/space/nyx_002/users/edann/test_tutorial/fs cd /autofs/space/nyx_002/users/edann/test_tutorial mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/bbr.pass1.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname curie.nmr.mgh.harvard.edu machine x86_64 user cy281 movvol /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/template.nii regfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/tmp.bbregister.172708/bbr.pass1.dat subject sub-BANDA001 dof 6 outregfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat UseMask 0 UseLH 1 UseRH 1 nsubsamp 1 PenaltySign -1 PenaltySlope 0.500000 PenaltyCenter 0.000000 surfname white GMProjFrac 0.500000 WMProjAbs 2.000000 lhcostfile (null) rhcostfile (null) interp trilinear (1) frame 0 TolPowell 0.000000 nMaxItersPowell 36 n1dmin 3 Profile 0 Gdiag_no -1 AddNoise 0 (0) SynthSeed 1689779096 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99808 -0.03616 0.05025 -1.03755; -0.05999 -0.36446 0.92929 -36.14234; -0.01529 -0.93052 -0.36593 -10.58528; 0.00000 0.00000 0.00000 1.00000; Loading mov ExcludeZeroVoxels 1 Reading in targ vol /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/orig.mgz 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 for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.973105 1 -25.0 -25.0 25.0 0.972602 2 -25.0 25.0 -25.0 0.961134 3 -25.0 25.0 25.0 0.957077 4 25.0 -25.0 -25.0 0.984348 5 25.0 -25.0 25.0 0.984012 6 25.0 25.0 -25.0 0.964715 7 25.0 25.0 25.0 0.985482 REL: 8 0.109932 7.782475 0.972809 rel = 0.113004 Initial costs ---------------- Number of surface hits 276186 WM Intensity 5070.3685 +/- 1579.2747 Ctx Intensity 6272.5171 +/- 1691.3218 Pct Contrast 22.0038 +/- 16.7939 Cost 0.1099 RelCost 0.1130 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1158 0.1158 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1148 0.1148 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.1141 0.1141 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1136 0.1136 0.0 37 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.0000 0.1135 0.1135 0.0 91 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.0000 0.1126 0.1126 0.0 92 -0.1000 0.0000 -0.1000 0.0000 -0.1000 0.1000 0.1125 0.1125 0.0 94 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1123 0.1123 0.0 283 0.0000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1120 0.1120 0.0 337 0.0000 0.0000 -0.1000 0.0000 0.0000 0.0000 0.1112 0.1112 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1103 0.1103 0.0 Brute Force -------------------------- Min cost was 0.110314 Number of iterations 729 Search time 1.041267 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 0.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 0 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.109932 7 -0.089 0.000 0.000 0.000 0.000 0.000 0.1092750508 8 -0.075 0.000 0.000 0.000 0.000 0.000 0.1092481487 9 -0.074 0.000 0.000 0.000 0.000 0.000 0.1092479998 17 -0.074 0.043 0.000 0.000 0.000 0.000 0.1091961620 18 -0.074 0.028 0.000 0.000 0.000 0.000 0.1091792719 27 -0.074 0.028 -0.059 0.000 0.000 0.000 0.1088302985 28 -0.074 0.028 -0.061 0.000 0.000 0.000 0.1088270344 29 -0.074 0.028 -0.069 0.000 0.000 0.000 0.1088226958 39 -0.074 0.028 -0.069 -0.004 0.000 0.000 0.1088220631 40 -0.074 0.028 -0.069 -0.003 0.000 0.000 0.1088219827 48 -0.074 0.028 -0.069 -0.003 -0.009 0.000 0.1088105315 49 -0.074 0.028 -0.069 -0.003 -0.011 0.000 0.1088097963 50 -0.074 0.028 -0.069 -0.003 -0.012 0.000 0.1088097425 58 -0.074 0.028 -0.069 -0.003 -0.012 0.076 0.1085508957 59 -0.074 0.028 -0.069 -0.003 -0.012 0.069 0.1085505316 60 -0.074 0.028 -0.069 -0.003 -0.012 0.072 0.1085501785 61 -0.074 0.028 -0.069 -0.003 -0.012 0.071 0.1085500633 powell nthiter 1: fret = 0.108550 70 -0.073 0.028 -0.069 -0.003 -0.012 0.071 0.1085499563 79 -0.073 0.025 -0.069 -0.003 -0.012 0.071 0.1085491736 80 -0.073 0.024 -0.069 -0.003 -0.012 0.071 0.1085491092 89 -0.073 0.024 -0.072 -0.003 -0.012 0.071 0.1085479148 90 -0.073 0.024 -0.073 -0.003 -0.012 0.071 0.1085478667 99 -0.073 0.024 -0.073 -0.002 -0.012 0.071 0.1085478275 100 -0.073 0.024 -0.073 -0.001 -0.012 0.071 0.1085477728 114 -0.073 0.024 -0.073 -0.001 -0.008 0.071 0.1085455580 123 -0.073 0.024 -0.073 -0.001 -0.008 0.074 0.1085452772 powell nthiter 2: fret = 0.108545 134 -0.074 0.024 -0.073 -0.001 -0.008 0.074 0.1085451603 171 -0.074 0.024 -0.073 -0.001 -0.007 0.074 0.1085451566 powell nthiter 3: fret = 0.108545 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 0.972904 1 -25.0 -25.0 25.0 0.972701 2 -25.0 25.0 -25.0 0.961375 3 -25.0 25.0 25.0 0.957526 4 25.0 -25.0 -25.0 0.983833 5 25.0 -25.0 25.0 0.984269 6 25.0 25.0 -25.0 0.964093 7 25.0 25.0 25.0 0.983964 REL: 8 0.108545 7.780665 0.972583 rel = 0.111605 Number of iterations 3 Min cost was 0.108545 Number of FunctionCalls 236 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 14.619716 sec Parameters at optimum (transmm) -0.07377 0.02446 -0.07282 Parameters at optimum (rotdeg) -0.00066 -0.00677 0.07369 Final costs ---------------- Number of surface hits 276186 WM Intensity 5070.7592 +/- 1575.3173 Ctx Intensity 6273.8557 +/- 1690.0131 Pct Contrast 22.0078 +/- 16.7009 Cost 0.1085 RelCost 0.1130 Reg at min cost was 0.99816 -0.03558 0.04910 -1.06358; -0.05870 -0.36451 0.92935 -36.11930; -0.01517 -0.93052 -0.36593 -10.65780; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat, type = 14 Original Reg 0.99808 -0.03616 0.05025 -1.03755; -0.05999 -0.36446 0.92929 -36.14234; -0.01529 -0.93052 -0.36593 -10.58528; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00008 -0.00058 0.00115 0.02603; -0.00128 0.00006 -0.00006 -0.02304; -0.00012 0.00000 0.00000 0.07252; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.112545 Computing change in rh position Surface-RMS-Diff-mm 0.117294 0.022460 0.168350 mri_segreg done MinCost: 0.108545 5070.759162 6273.855728 22.007802 tkregister2_cmdl --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat --noedit --ltaout /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.lta INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 ---- Input registration matrix -------- 0.99816 -0.03558 0.04910 -1.06358; -0.05870 -0.36451 0.92935 -36.11930; -0.01517 -0.93052 -0.36593 -10.65780; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA001/mri/orig.mgz Ttarg: -------------------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; INFO: loading movable /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz Tmov: -------------------- -1.50000 0.00000 0.00000 105.00000; 0.00000 0.00000 1.50000 -69.00000; 0.00000 -1.50000 0.00000 105.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.99816 -0.03558 0.04910 -1.06358; -0.05870 -0.36451 0.92935 -36.11930; -0.01517 -0.93052 -0.36593 -10.65780; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-BANDA001 RegMat --------------------------- 0.99816 -0.03558 0.04910 -1.06358; -0.05870 -0.36451 0.92935 -36.11930; -0.01517 -0.93052 -0.36593 -10.65780; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jul 12 17:31:55 EDT 2023 Ended at Wed Jul 12 17:32:43 EDT 2023 BBR-Run-Time-Sec 48 bbregister Done To check results, run: tkregisterfv --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA001/dmri/xfms/diff2anatorig.bbr.lta --surfs --sd /autofs/space/nyx_002/users/edann/test_tutorial/fs