Logfile for bbregister Wed Jul 12 22:46:24 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-BANDA002 --init-fsl --dti --6 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/lowb.nii.gz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/lowb.nii.gz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii reading from /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/lowb.nii.gz... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995812, -0.0531134, -0.0744134) j_ras = (-0.0778475, 0.919405, 0.385532) k_ras = (-0.0479391, -0.38971, 0.919689) writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii... fslregister --s sub-BANDA002 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --niters 1 --maxangle 90 --tmp /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat.fslregister.log Wed Jul 12 22:46:24 EDT 2023 --s sub-BANDA002 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --niters 1 --maxangle 90 --tmp /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/mri/brainmask.mgz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/refvol.fslregister.nii mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA002/mri/brainmask.mgz /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/refvol.fslregister.nii reading from /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA002/mri/brainmask.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1.11759e-08, 0) j_ras = (0, 0, -1) k_ras = (-3.72529e-09, 1, 2.32831e-09) writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/movvol.fslregister.nii --frame 0 mri_convert /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/movvol.fslregister.nii --frame 0 reading from /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii... TR=3230.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.995812, -0.0531134, -0.0744134) j_ras = (-0.0778475, 0.919405, 0.385532) k_ras = (-0.0479391, -0.38971, 0.919689) keeping frame 0 writing to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/movvol.fslregister.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/reg0.54189.dat --targ brainmask --fstarg --regheader --fslregout /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat.fsl.mat0 --s sub-BANDA002 --noedit target volume brainmask movable volume /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/movvol.fslregister.nii reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/reg0.54189.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 INFO: loading target /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA002/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-BANDA002/dmri/xfms/tmp.bbregister.54148/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) -------- 0.99581 0.05311 0.07441 -0.39890; -0.04794 -0.38971 0.91969 -23.81850; 0.07785 -0.91940 -0.38553 -8.84590; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99581 0.05311 0.07441 -0.39890; -0.04794 -0.38971 0.91969 -23.81850; 0.07785 -0.91940 -0.38553 -8.84590; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = sub-BANDA002 RegMat --------------------------- 0.99581 0.05311 0.07441 -0.39890; -0.04794 -0.38971 0.91969 -23.81850; 0.07785 -0.91940 -0.38553 -8.84590; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -3.375, ref det = -1 Wed Jul 12 22:46:25 EDT 2023 /autofs/space/nyx_002/users/edann/test_tutorial flirt.fsl -ref /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/refvol.fslregister.nii -in /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat.fsl.mat0 Wed Jul 12 22:46:34 EDT 2023 /autofs/space/nyx_002/users/edann/test_tutorial flirt.fsl -ref /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/refvol.fslregister.nii -in /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat.fsl.mat -init /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/7.3.2/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s sub-BANDA002 --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --targ brainmask --fstarg --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --fslreg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.99615 0.07404 0.04701 11.72650; 0.07356 -0.41353 -0.90751 206.10201; -0.04775 0.90748 -0.41738 49.17200; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- target volume brainmask movable volume /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/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-BANDA002/dmri/xfms/tmp.bbregister.54148/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) -------- 0.99615 0.04775 0.07356 -1.31587; -0.04701 -0.41738 0.90751 -25.55643; 0.07404 -0.90748 -0.41353 -7.44051; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.99615 0.04775 0.07356 -1.31587; -0.04701 -0.41738 0.90751 -25.55643; 0.07404 -0.90748 -0.41353 -7.44051; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = sub-BANDA002 RegMat --------------------------- 0.99615 0.04775 0.07356 -1.31587; -0.04701 -0.41738 0.90751 -25.55643; 0.07404 -0.90748 -0.41353 -7.44051; 0.00000 0.00000 0.00000 1.00000; (standard_in) 1: illegal character: N (standard_in) 1: syntax error Started at Wed Jul 12 22:46:24 EDT 2023 Ended at Wed Jul 12 22:46:49 EDT 2023 fslregister Done To check results, run: tkregisterfv --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --surf orig mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii regfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/reg.init.dat subject sub-BANDA002 dof 6 outregfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/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 1689872973 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99615 0.04775 0.07356 -1.31587; -0.04701 -0.41738 0.90751 -25.55643; 0.07404 -0.90748 -0.41353 -7.44051; 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-BANDA002/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 0.963193 1 -25.0 -25.0 25.0 0.975839 2 -25.0 25.0 -25.0 0.980628 3 -25.0 25.0 25.0 0.958914 4 25.0 -25.0 -25.0 1.013025 5 25.0 -25.0 25.0 0.977071 6 25.0 25.0 -25.0 1.021813 7 25.0 25.0 25.0 0.988170 REL: 8 0.154967 7.878653 0.984832 rel = 0.157353 Initial costs ---------------- Number of surface hits 2434 WM Intensity 5402.7431 +/- 1640.0735 Ctx Intensity 6698.5086 +/- 1769.9045 Pct Contrast 22.2075 +/- 16.8748 Cost 0.1550 RelCost 0.1574 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9803 0.9803 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9500 0.9500 0.0 2 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.9328 0.9328 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.8997 0.8997 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8681 0.8681 0.0 33 -4.0000 -4.0000 0.0000 -4.0000 4.0000 -4.0000 0.8532 0.8532 0.0 34 -4.0000 -4.0000 0.0000 -4.0000 4.0000 0.0000 0.8521 0.8521 0.0 118 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.8236 0.8236 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.8183 0.8183 0.0 124 -4.0000 0.0000 0.0000 0.0000 4.0000 0.0000 0.7825 0.7825 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.7075 0.7075 0.0 292 0.0000 -4.0000 0.0000 4.0000 0.0000 0.0000 0.7067 0.7067 0.0 361 0.0000 0.0000 0.0000 0.0000 -4.0000 0.0000 0.6671 0.6671 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6021 0.6021 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1550 0.1550 0.0 Brute Force -------------------------- Min cost was 0.154967 Number of iterations 729 Search time 1.012657 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 = 0.154967 7 0.030 0.000 0.000 0.000 0.000 0.000 0.1539449581 8 0.104 0.000 0.000 0.000 0.000 0.000 0.1525413685 10 0.115 0.000 0.000 0.000 0.000 0.000 0.1524311591 12 0.133 0.000 0.000 0.000 0.000 0.000 0.1523449172 20 0.133 -0.618 0.000 0.000 0.000 0.000 0.1090512621 22 0.133 -0.571 0.000 0.000 0.000 0.000 0.1089035424 23 0.133 -0.583 0.000 0.000 0.000 0.000 0.1088802667 24 0.133 -0.584 0.000 0.000 0.000 0.000 0.1088800081 32 0.133 -0.584 0.090 0.000 0.000 0.000 0.1087494281 33 0.133 -0.584 0.053 0.000 0.000 0.000 0.1086568651 35 0.133 -0.584 0.033 0.000 0.000 0.000 0.1086444806 36 0.133 -0.584 0.041 0.000 0.000 0.000 0.1086388514 37 0.133 -0.584 0.040 0.000 0.000 0.000 0.1086388029 45 0.133 -0.584 0.040 0.179 0.000 0.000 0.1063248657 46 0.133 -0.584 0.040 0.173 0.000 0.000 0.1062532690 47 0.133 -0.584 0.040 0.135 0.000 0.000 0.1060106087 51 0.133 -0.584 0.040 0.134 0.000 0.000 0.1060104777 61 0.133 -0.584 0.040 0.134 -0.055 0.000 0.1053751786 62 0.133 -0.584 0.040 0.134 -0.056 0.000 0.1053749006 70 0.133 -0.584 0.040 0.134 -0.056 0.105 0.1046487815 72 0.133 -0.584 0.040 0.134 -0.056 0.102 0.1046470104 75 0.133 -0.584 0.040 0.134 -0.056 0.096 0.1046465710 76 0.133 -0.584 0.040 0.134 -0.056 0.098 0.1046464032 powell nthiter 1: fret = 0.104646 87 0.164 -0.584 0.040 0.134 -0.056 0.098 0.1045950662 88 0.152 -0.584 0.040 0.134 -0.056 0.098 0.1045435034 99 0.152 -0.606 0.040 0.134 -0.056 0.098 0.1045397912 100 0.152 -0.596 0.040 0.134 -0.056 0.098 0.1045278067 109 0.152 -0.596 0.069 0.134 -0.056 0.098 0.1042127926 110 0.152 -0.596 0.091 0.134 -0.056 0.098 0.1040944372 112 0.152 -0.596 0.107 0.134 -0.056 0.098 0.1040933279 113 0.152 -0.596 0.099 0.134 -0.056 0.098 0.1040834729 114 0.152 -0.596 0.098 0.134 -0.056 0.098 0.1040833114 126 0.152 -0.596 0.098 0.136 -0.056 0.098 0.1040819465 127 0.152 -0.596 0.098 0.137 -0.056 0.098 0.1040819352 136 0.152 -0.596 0.098 0.137 -0.046 0.098 0.1040540270 138 0.152 -0.596 0.098 0.137 -0.044 0.098 0.1040536290 146 0.152 -0.596 0.098 0.137 -0.044 0.084 0.1040514820 148 0.152 -0.596 0.098 0.137 -0.044 0.085 0.1040514063 149 0.152 -0.596 0.098 0.137 -0.044 0.086 0.1040510979 powell nthiter 2: fret = 0.104051 160 0.139 -0.596 0.098 0.137 -0.044 0.086 0.1039853241 162 0.140 -0.596 0.098 0.137 -0.044 0.086 0.1039848568 174 0.140 -0.599 0.098 0.137 -0.044 0.086 0.1039837009 195 0.140 -0.599 0.098 0.136 -0.044 0.086 0.1039834932 213 0.140 -0.599 0.098 0.136 -0.044 0.087 0.1039811781 214 0.140 -0.599 0.098 0.136 -0.044 0.103 0.1039684384 216 0.140 -0.599 0.098 0.136 -0.044 0.099 0.1039683881 218 0.140 -0.599 0.098 0.136 -0.044 0.100 0.1039683044 219 0.140 -0.599 0.098 0.136 -0.044 0.101 0.1039682403 220 0.127 -0.602 0.098 0.135 -0.044 0.117 0.1039497044 226 0.132 -0.601 0.098 0.136 -0.044 0.111 0.1039485064 227 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039472772 228 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039472191 230 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039470704 232 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039469843 233 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039469771 234 0.130 -0.601 0.098 0.136 -0.044 0.113 0.1039469660 powell nthiter 3: fret = 0.103947 244 0.130 -0.601 0.098 0.136 -0.044 0.122 0.1039443747 246 0.130 -0.601 0.098 0.136 -0.044 0.120 0.1039442140 266 0.130 -0.601 0.100 0.136 -0.044 0.120 0.1039438174 277 0.130 -0.601 0.100 0.140 -0.044 0.120 0.1039382738 279 0.130 -0.601 0.100 0.141 -0.044 0.120 0.1039377601 288 0.130 -0.601 0.100 0.141 -0.040 0.120 0.1039351350 289 0.130 -0.601 0.100 0.141 -0.041 0.120 0.1039349021 297 0.129 -0.601 0.100 0.141 -0.041 0.121 0.1039346909 301 0.129 -0.601 0.100 0.141 -0.041 0.121 0.1039344846 303 0.129 -0.601 0.100 0.141 -0.041 0.121 0.1039343975 powell nthiter 4: fret = 0.103934 315 0.129 -0.601 0.100 0.141 -0.041 0.125 0.1039341479 316 0.129 -0.601 0.100 0.141 -0.041 0.124 0.1039341065 326 0.129 -0.600 0.100 0.141 -0.041 0.124 0.1039338560 337 0.129 -0.600 0.101 0.141 -0.041 0.124 0.1039336748 348 0.129 -0.600 0.101 0.142 -0.041 0.124 0.1039335946 358 0.129 -0.600 0.101 0.142 -0.039 0.124 0.1039333678 372 0.129 -0.600 0.101 0.142 -0.039 0.124 0.1039333659 373 0.129 -0.600 0.101 0.142 -0.039 0.124 0.1039333606 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.968600 1 -25.0 -25.0 25.0 0.976477 2 -25.0 25.0 -25.0 0.993285 3 -25.0 25.0 25.0 0.968564 4 25.0 -25.0 -25.0 1.012746 5 25.0 -25.0 25.0 0.966736 6 25.0 25.0 -25.0 1.014413 7 25.0 25.0 25.0 0.994034 REL: 8 0.103933 7.894855 0.986857 rel = 0.105318 Number of iterations 4 Min cost was 0.103933 Number of FunctionCalls 374 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.520887 sec Parameters at optimum (transmm) 0.12894 -0.60019 0.10083 Parameters at optimum (rotdeg) 0.14237 -0.03930 0.12383 Final costs ---------------- Number of surface hits 2434 WM Intensity 5344.0078 +/- 1609.5279 Ctx Intensity 6659.7136 +/- 1736.1276 Pct Contrast 22.7452 +/- 16.1551 Cost 0.1039 RelCost 0.1574 Reg at min cost was 0.99620 0.04927 0.07188 -1.12659; -0.04504 -0.41502 0.90870 -26.14082; 0.07460 -0.90848 -0.41122 -7.40405; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/bbr.pass1.dat, type = 14 Original Reg 0.99615 0.04775 0.07356 -1.31587; -0.04701 -0.41738 0.90751 -25.55643; 0.07404 -0.90748 -0.41353 -7.44051; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00005 -0.00152 0.00168 -0.18929; -0.00197 -0.00236 -0.00118 0.58440; -0.00057 0.00100 -0.00231 -0.03645; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.699537 Computing change in rh position Surface-RMS-Diff-mm 0.648602 0.102409 0.860576 mri_segreg done mri_segreg --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/bbr.pass1.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii --init-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/bbr.pass1.dat --out-reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/xfms/diff2anatorig.bbr.dat.mincost --dof 6 --nmax 36 --param /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/xfms/tmp.bbregister.54148/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-BANDA002/dmri/xfms/tmp.bbregister.54148/template.nii regfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/tmp.bbregister.54148/bbr.pass1.dat subject sub-BANDA002 dof 6 outregfile /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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 1689579949 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.99620 0.04927 0.07188 -1.12659; -0.04504 -0.41502 0.90870 -26.14082; 0.07460 -0.90848 -0.41122 -7.40405; 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-BANDA002/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 0.968561 1 -25.0 -25.0 25.0 0.978324 2 -25.0 25.0 -25.0 0.978772 3 -25.0 25.0 25.0 0.959206 4 25.0 -25.0 -25.0 1.013145 5 25.0 -25.0 25.0 0.981847 6 25.0 25.0 -25.0 0.988035 7 25.0 25.0 25.0 1.001182 REL: 8 0.113554 7.869073 0.983634 rel = 0.115443 Initial costs ---------------- Number of surface hits 243368 WM Intensity 5364.9903 +/- 1645.2536 Ctx Intensity 6680.6525 +/- 1777.7064 Pct Contrast 22.6217 +/- 17.0375 Cost 0.1136 RelCost 0.1154 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1122 0.1122 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.1114 0.1114 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.1114 0.1114 0.0 9 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 -0.1000 0.1085 0.1085 0.0 10 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.1084 0.1084 0.0 12 -0.1000 -0.1000 -0.1000 0.0000 0.0000 -0.1000 0.1083 0.1083 0.0 18 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 -0.1000 0.1079 0.1079 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.1076 0.1076 0.0 40 -0.1000 -0.1000 0.0000 0.0000 0.0000 0.0000 0.1064 0.1064 0.0 118 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1060 0.1060 0.0 121 -0.1000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1053 0.1053 0.0 361 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0000 0.1053 0.1053 0.0 362 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1000 0.1051 0.1051 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.1045 0.1045 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.1039 0.1039 0.0 Brute Force -------------------------- Min cost was 0.103933 Number of iterations 729 Search time 1.033848 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 = 0.113554 7 -0.036 0.000 0.000 0.000 0.000 0.000 0.1134477215 8 -0.029 0.000 0.000 0.000 0.000 0.000 0.1134422107 17 -0.029 0.092 0.000 0.000 0.000 0.000 0.1126176744 18 -0.029 0.084 0.000 0.000 0.000 0.000 0.1126172587 19 -0.029 0.088 0.000 0.000 0.000 0.000 0.1126151867 28 -0.029 0.088 0.027 0.000 0.000 0.000 0.1125324950 29 -0.029 0.088 0.026 0.000 0.000 0.000 0.1125322677 37 -0.029 0.088 0.026 0.125 0.000 0.000 0.1109734200 46 -0.029 0.088 0.026 0.125 -0.003 0.000 0.1109621871 47 -0.029 0.088 0.026 0.125 -0.018 0.000 0.1109381182 56 -0.029 0.088 0.026 0.125 -0.018 -0.103 0.1101721115 57 -0.029 0.088 0.026 0.125 -0.018 -0.105 0.1101717784 58 -0.029 0.088 0.026 0.125 -0.018 -0.106 0.1101716722 powell nthiter 1: fret = 0.110172 68 -0.052 0.088 0.026 0.125 -0.018 -0.106 0.1099725053 69 -0.077 0.088 0.026 0.125 -0.018 -0.106 0.1099275177 70 -0.071 0.088 0.026 0.125 -0.018 -0.106 0.1099212391 79 -0.071 0.106 0.026 0.125 -0.018 -0.106 0.1099161380 80 -0.071 0.098 0.026 0.125 -0.018 -0.106 0.1099064248 89 -0.071 0.098 0.001 0.125 -0.018 -0.106 0.1098056540 90 -0.071 0.098 -0.004 0.125 -0.018 -0.106 0.1098041504 91 -0.071 0.098 -0.003 0.125 -0.018 -0.106 0.1098040449 99 -0.071 0.098 -0.003 0.136 -0.018 -0.106 0.1097827837 100 -0.071 0.098 -0.003 0.139 -0.018 -0.106 0.1097825956 102 -0.071 0.098 -0.003 0.138 -0.018 -0.106 0.1097824803 103 -0.071 0.098 -0.003 0.137 -0.018 -0.106 0.1097824713 111 -0.071 0.098 -0.003 0.137 -0.017 -0.106 0.1097822424 119 -0.071 0.098 -0.003 0.137 -0.017 -0.115 0.1097611665 120 -0.071 0.098 -0.003 0.137 -0.017 -0.127 0.1097552093 121 -0.071 0.098 -0.003 0.137 -0.017 -0.124 0.1097544374 powell nthiter 2: fret = 0.109754 132 -0.079 0.098 -0.003 0.137 -0.017 -0.124 0.1097526892 133 -0.076 0.098 -0.003 0.137 -0.017 -0.124 0.1097508252 143 -0.076 0.101 -0.003 0.137 -0.017 -0.124 0.1097490118 153 -0.076 0.101 -0.007 0.137 -0.017 -0.124 0.1097471985 155 -0.076 0.101 -0.006 0.137 -0.017 -0.124 0.1097471487 163 -0.076 0.101 -0.006 0.138 -0.017 -0.124 0.1097465793 164 -0.076 0.101 -0.006 0.141 -0.017 -0.124 0.1097461277 184 -0.076 0.101 -0.006 0.141 -0.017 -0.127 0.1097458706 powell nthiter 3: fret = 0.109746 205 -0.076 0.102 -0.006 0.141 -0.017 -0.127 0.1097457647 214 -0.076 0.102 -0.008 0.141 -0.017 -0.127 0.1097455488 powell nthiter 4: fret = 0.109746 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.967409 1 -25.0 -25.0 25.0 0.978164 2 -25.0 25.0 -25.0 0.977464 3 -25.0 25.0 25.0 0.960204 4 25.0 -25.0 -25.0 1.011200 5 25.0 -25.0 25.0 0.980773 6 25.0 25.0 -25.0 0.988583 7 25.0 25.0 25.0 1.001297 REL: 8 0.109746 7.865094 0.983137 rel = 0.111628 Number of iterations 4 Min cost was 0.109746 Number of FunctionCalls 301 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 18.623851 sec Parameters at optimum (transmm) -0.07554 0.10245 -0.00812 Parameters at optimum (rotdeg) 0.14059 -0.01689 -0.12688 Final costs ---------------- Number of surface hits 243368 WM Intensity 5370.4795 +/- 1646.4226 Ctx Intensity 6690.7228 +/- 1774.9227 Pct Contrast 22.6977 +/- 16.9158 Cost 0.1097 RelCost 0.1154 Reg at min cost was 0.99607 0.04862 0.07402 -1.25777; -0.04743 -0.41290 0.90954 -26.01757; 0.07479 -0.90948 -0.40897 -7.47662; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/diff2anatorig.bbr.dat, type = 14 Original Reg 0.99620 0.04927 0.07188 -1.12659; -0.04504 -0.41502 0.90870 -26.14082; 0.07460 -0.90848 -0.41122 -7.40405; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00012 0.00065 -0.00213 0.13119; 0.00239 -0.00212 -0.00084 -0.12325; -0.00018 0.00100 -0.00225 0.07257; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.192233 Computing change in rh position Surface-RMS-Diff-mm 0.165764 0.071366 0.368597 mri_segreg done MinCost: 0.109746 5370.479477 6690.722808 22.697713 tkregister2_cmdl --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/diff2anatorig.bbr.dat --noedit --ltaout /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/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-BANDA002/dmri/lowb.nii.gz reg file /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/diff2anatorig.bbr.dat LoadVol 0 ZeroCRAS 0 7.3.2 Diagnostic Level -1 ---- Input registration matrix -------- 0.99607 0.04862 0.07402 -1.25777; -0.04743 -0.41290 0.90954 -26.01757; 0.07479 -0.90948 -0.40897 -7.47662; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/nyx_002/users/edann/test_tutorial/fs/sub-BANDA002/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-BANDA002/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 -------- 0.99607 0.04862 0.07402 -1.25777; -0.04743 -0.41290 0.90954 -26.01757; 0.07479 -0.90948 -0.40897 -7.47662; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999998 subject = sub-BANDA002 RegMat --------------------------- 0.99607 0.04862 0.07402 -1.25777; -0.04743 -0.41290 0.90954 -26.01757; 0.07479 -0.90948 -0.40897 -7.47662; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Wed Jul 12 22:46:24 EDT 2023 Ended at Wed Jul 12 22:47:18 EDT 2023 BBR-Run-Time-Sec 54 bbregister Done To check results, run: tkregisterfv --mov /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/lowb.nii.gz --reg /autofs/space/nyx_002/users/edann/test_tutorial/trc_cm/sub-BANDA002/dmri/xfms/diff2anatorig.bbr.lta --surfs --sd /autofs/space/nyx_002/users/edann/test_tutorial/fs