Logfile for bbregister 2021��� 05��� 28��� ��������� 11:17:14 CST setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC/ cd /home/yelab /usr/local/freesurfer/bin/bbregister --s pd_struc_recon --mov /media/yelab/data/PD/PD_Nii_withCBF/PD001/CBF/CBF.nii.gz --t1 --init-fsl --reg /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat bbregister 7.1.1 Linux yelab-Precision-5820-Tower 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert /media/yelab/data/PD/PD_Nii_withCBF/PD001/CBF/CBF.nii.gz /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii mri_convert /media/yelab/data/PD/PD_Nii_withCBF/PD001/CBF/CBF.nii.gz /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii reading from /media/yelab/data/PD/PD_Nii_withCBF/PD001/CBF/CBF.nii.gz... TR=1000.00, 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 /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii... fslregister --s pd_struc_recon --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --niters 1 --maxangle 90 --tmp /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov Log file is /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat.fslregister.log 2021��� 05��� 28��� ��������� 11:17:14 CST --s pd_struc_recon --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --niters 1 --maxangle 90 --tmp /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov fslregister 7.1.1 yelab-Precision-5820-Tower Linux yelab-Precision-5820-Tower 5.4.0-73-generic #82~18.04.1-Ubuntu SMP Fri Apr 16 15:10:02 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /home/yelab mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC//pd_struc_recon/mri/brainmask.mgz /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/refvol.fslregister.nii mri_convert /media/yelab/data/PD/PD_Nii/sub1/STRUC//pd_struc_recon/mri/brainmask.mgz /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/refvol.fslregister.nii reading from /media/yelab/data/PD/PD_Nii/sub1/STRUC//pd_struc_recon/mri/brainmask.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 9.31323e-10, 0) j_ras = (7.45058e-09, -2.32831e-10, -1) k_ras = (0, 1, -1.16415e-09) writing to /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/refvol.fslregister.nii... -------------------------------------- /home/yelab mri_convert /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii --frame 0 mri_convert /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii --frame 0 reading from /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii... TR=1000.00, 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 /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii... Mov determinant is -1 /home/yelab tkregister2_cmdl --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii --reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/reg0.6670.dat --regheader --fslregout /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat.fsl.mat0 --s pd_struc_recon --noedit INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii reg file /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/reg0.6670.dat LoadVol 0 ZeroCRAS 0 7.1.1 Diagnostic Level -1 INFO: loading target /media/yelab/data/PD/PD_Nii/sub1/STRUC//pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii Tmov: -------------------- -1.00000 0.00000 0.00000 91.00000; 0.00000 0.00000 1.00000 -91.00000; 0.00000 -1.00000 0.00000 109.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 1.00000 0.00000 -0.00000 -3.14130; 0.00000 -0.00000 1.00000 -9.12019; 0.00000 -1.00000 -0.00000 -29.39159; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 1.00000 0.00000 -0.00000 -3.14130; 0.00000 -0.00000 1.00000 -9.12019; 0.00000 -1.00000 -0.00000 -29.39159; 0.00000 0.00000 0.00000 1.00000; Determinant 1 subject = pd_struc_recon RegMat --------------------------- 1.00000 0.00000 -0.00000 -3.14130; 0.00000 -0.00000 1.00000 -9.12019; 0.00000 -1.00000 -0.00000 -29.39159; 0.00000 0.00000 0.00000 1.00000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -1, ref det = -1 2021��� 05��� 28��� ��������� 11:17:15 CST /home/yelab flirt.fsl -ref /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/refvol.fslregister.nii -in /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/fsl.5.0.2.xyztrans.sch -init /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat.fsl.mat0 2021��� 05��� 28��� ��������� 11:17:42 CST /home/yelab flirt.fsl -ref /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/refvol.fslregister.nii -in /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat.fsl.mat -init /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch tkregister2_cmdl --s pd_struc_recon --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --fslreg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat.fsl.mat --noedit ---- FSL registration matrix -------- 0.95680 0.28080 -0.07542 19.37570; -0.26903 0.75667 -0.59588 132.41100; -0.11025 0.59043 0.79952 2.31983; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii reg file /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat LoadVol 0 ZeroCRAS 0 7.1.1 Diagnostic Level -1 INFO: loading target /media/yelab/data/PD/PD_Nii/sub1/STRUC//pd_struc_recon/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 /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii Tmov: -------------------- -1.00000 0.00000 0.00000 91.00000; 0.00000 0.00000 1.00000 -91.00000; 0.00000 -1.00000 0.00000 109.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 FSLOUTPUTTYPE NIFTI fsl2TkReg: mov det = -1, ref det = -1 ---- Input registration matrix (computed) -------- 0.95680 0.11025 -0.26903 -0.26177; 0.07542 0.79952 0.59588 3.91978; 0.28079 -0.59043 0.75667 7.63083; 0.00000 0.00000 0.00000 1.00000; --------------------------------------- ---- Input registration matrix -------- 0.95680 0.11025 -0.26903 -0.26177; 0.07542 0.79952 0.59588 3.91978; 0.28079 -0.59043 0.75667 7.63083; 0.00000 0.00000 0.00000 1.00000; Determinant 0.999999 subject = pd_struc_recon RegMat --------------------------- 0.95680 0.11025 -0.26903 -0.26177; 0.07542 0.79952 0.59588 3.91978; 0.28079 -0.59043 0.75667 7.63083; 0.00000 0.00000 0.00000 1.00000; Started at 2021��� 05��� 28��� ��������� 11:17:14 CST Ended at 2021��� 05��� 28��� ��������� 11:18:26 CST fslregister Done To check results, run: tkregisterfv --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --surf orig mri_segreg --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --init-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --out-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/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 --wm-gt-gm 0.5 7.1.1 setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC/ cd /home/yelab mri_segreg --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --init-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat --out-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/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 --wm-gt-gm 0.5 sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab movvol /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii regfile /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.init.dat subject pd_struc_recon dof 6 outregfile /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/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 1622494784 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.95680 0.11025 -0.26903 -0.26177; 0.07542 0.79952 0.59588 3.91978; 0.28079 -0.59043 0.75667 7.63083; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.967311 1 -25.0 -25.0 25.0 0.968058 2 -25.0 25.0 -25.0 0.927251 3 -25.0 25.0 25.0 0.984480 4 25.0 -25.0 -25.0 0.963680 5 25.0 -25.0 25.0 0.960480 6 25.0 25.0 -25.0 0.965043 7 25.0 25.0 25.0 0.933411 REL: 8 0.954670 7.669714 0.958714 rel = 0.995781 Initial costs ---------------- Number of surface hits 2307 WM Intensity 26.7165 +/- 16.1717 Ctx Intensity 25.9313 +/- 16.2489 Pct Contrast -3.2958 +/- 47.6798 Cost 0.9547 RelCost 0.9958 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9758 0.9758 0.0 1 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.0000 0.9697 0.9697 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9484 0.9484 0.0 31 -4.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.9460 0.9460 0.0 45 -4.0000 -4.0000 0.0000 4.0000 -4.0000 -4.0000 0.9319 0.9319 0.0 173 -4.0000 4.0000 -4.0000 0.0000 -4.0000 4.0000 0.9205 0.9205 0.0 476 0.0000 4.0000 4.0000 0.0000 4.0000 4.0000 0.9132 0.9132 0.0 Brute Force -------------------------- Min cost was 0.913177 Number of iterations 729 Search time 1.056676 sec Parameters at best (transmm, rotdeg) 0.000 4.000 4.000 0.000 4.000 4.000 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 4 2 4 3 0 4 4 5 4 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000100 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.913177 5 -0.618 4.000 4.000 0.000 4.000 4.000 0.9088300730 9 -0.558 4.000 4.000 0.000 4.000 4.000 0.9076416926 11 -0.579 4.000 4.000 0.000 4.000 4.000 0.9070040206 13 -0.582 4.000 4.000 0.000 4.000 4.000 0.9069975725 14 -0.581 4.000 4.000 0.000 4.000 4.000 0.9069967819 26 -0.581 3.981 4.000 0.000 4.000 4.000 0.9069827646 28 -0.581 3.990 4.000 0.000 4.000 4.000 0.9069767218 30 -0.581 3.994 4.000 0.000 4.000 4.000 0.9069744507 32 -0.581 3.993 4.000 0.000 4.000 4.000 0.9069743144 43 -0.581 3.993 3.989 0.000 4.000 4.000 0.9068582658 44 -0.581 3.993 3.986 0.000 4.000 4.000 0.9068339780 45 -0.581 3.993 3.981 0.000 4.000 4.000 0.9068116239 57 -0.581 3.993 3.981 0.003 4.000 4.000 0.9067919202 58 -0.581 3.993 3.981 0.014 4.000 4.000 0.9067135357 63 -0.581 3.993 3.981 0.015 4.000 4.000 0.9067074566 69 -0.581 3.993 3.981 0.015 4.382 4.000 0.9027824067 70 -0.581 3.993 3.981 0.015 4.449 4.000 0.9027302060 71 -0.581 3.993 3.981 0.015 4.434 4.000 0.9021341611 72 -0.581 3.993 3.981 0.015 4.416 4.000 0.9020423922 78 -0.581 3.993 3.981 0.015 4.417 4.000 0.9020376313 87 -0.581 3.993 3.981 0.015 4.417 4.001 0.9020081654 89 -0.581 3.993 3.981 0.015 4.417 4.022 0.9016318257 90 -0.581 3.993 3.981 0.015 4.417 4.029 0.9015373903 96 -1.162 3.985 3.961 0.029 4.834 4.058 0.8996655108 101 -1.522 3.981 3.949 0.038 5.092 4.076 0.8956182180 103 -1.455 3.982 3.951 0.037 5.044 4.073 0.8932421230 106 -1.473 3.982 3.951 0.037 5.057 4.073 0.8929795691 109 -1.474 3.982 3.951 0.037 5.057 4.073 0.8929787351 powell nthiter 1: fret = 0.892979 118 -1.474 3.982 3.951 0.037 5.057 3.931 0.8898988866 119 -1.474 3.982 3.951 0.037 5.057 3.822 0.8893096308 122 -1.474 3.982 3.951 0.037 5.057 3.769 0.8886918800 126 -1.474 3.982 3.951 0.037 5.057 3.765 0.8886868785 135 -1.474 3.857 3.951 0.037 5.057 3.765 0.8872429492 136 -1.474 3.841 3.951 0.037 5.057 3.765 0.8871230554 141 -1.474 3.843 3.951 0.037 5.057 3.765 0.8871198349 149 -1.474 3.843 4.333 0.037 5.057 3.765 0.8858364110 150 -1.474 3.843 4.211 0.037 5.057 3.765 0.8818852403 156 -1.474 3.843 4.214 0.037 5.057 3.765 0.8818810627 164 -1.474 3.843 4.213 -0.103 5.057 3.765 0.8787051302 166 -1.474 3.843 4.213 -0.068 5.057 3.765 0.8784402748 169 -1.474 3.843 4.213 -0.047 5.057 3.765 0.8779193339 174 -1.474 3.843 4.213 -0.048 5.057 3.765 0.8778943017 187 -1.474 3.843 4.213 -0.048 5.055 3.765 0.8778083779 199 -1.461 3.843 4.214 -0.048 5.046 3.764 0.8776895023 202 -1.458 3.844 4.214 -0.048 5.044 3.764 0.8776720244 powell nthiter 2: fret = 0.877672 215 -1.458 3.844 4.214 -0.048 5.044 3.767 0.8776528512 216 -1.458 3.844 4.214 -0.048 5.044 3.770 0.8776373899 218 -1.458 3.844 4.214 -0.048 5.044 3.774 0.8776190879 219 -1.458 3.844 4.214 -0.048 5.044 3.775 0.8776187798 228 -1.458 3.829 4.214 -0.048 5.044 3.775 0.8772614994 230 -1.458 3.825 4.214 -0.048 5.044 3.775 0.8772032146 231 -1.458 3.823 4.214 -0.048 5.044 3.775 0.8771640149 233 -1.458 3.821 4.214 -0.048 5.044 3.775 0.8771390519 234 -1.458 3.819 4.214 -0.048 5.044 3.775 0.8771258358 235 -1.458 3.818 4.214 -0.048 5.044 3.775 0.8771161276 246 -1.458 3.818 4.215 -0.048 5.044 3.775 0.8771067390 249 -1.458 3.818 4.216 -0.048 5.044 3.775 0.8770999389 288 -1.457 3.818 4.216 -0.048 5.043 3.775 0.8770940501 289 -1.457 3.818 4.216 -0.048 5.043 3.775 0.8770880665 powell nthiter 3: fret = 0.877088 Powell done niters = 3 Computing relative cost 0 -25.0 -25.0 -25.0 0.966493 1 -25.0 -25.0 25.0 1.000994 2 -25.0 25.0 -25.0 0.914226 3 -25.0 25.0 25.0 1.004817 4 25.0 -25.0 -25.0 0.974532 5 25.0 -25.0 25.0 0.989482 6 25.0 25.0 -25.0 0.978557 7 25.0 25.0 25.0 0.971512 REL: 8 0.877088 7.800614 0.975077 rel = 0.899507 Number of iterations 3 Min cost was 0.877088 Number of FunctionCalls 377 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.526108 sec Parameters at optimum (transmm) -1.45655 3.81841 4.21602 Parameters at optimum (rotdeg) -0.04832 5.04289 3.77512 Final costs ---------------- Number of surface hits 2259 WM Intensity 25.8022 +/- 12.1597 Ctx Intensity 24.9102 +/- 13.3715 Pct Contrast -6.9843 +/- 48.8051 Cost 0.8771 RelCost 0.9958 Reg at min cost was 0.97067 0.00513 -0.24036 -1.30623; 0.13987 0.80110 0.58196 7.76308; 0.19554 -0.59851 0.77688 11.83703; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/bbr.pass1.dat, type = 14 Original Reg 0.95680 0.11025 -0.26903 -0.26177; 0.07542 0.79952 0.59588 3.91978; 0.28079 -0.59043 0.75667 7.63083; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.01387 0.10512 -0.02867 1.04446; -0.06445 -0.00158 0.01392 -3.84330; 0.08525 0.00808 -0.02022 -4.20620; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 8.372769 Computing change in rh position Surface-RMS-Diff-mm 7.898210 1.170424 11.065359 mri_segreg done mri_segreg --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --init-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/bbr.pass1.dat --out-reg /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat.mincost --dof 6 --nmax 36 --param /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --wm-gt-gm 0.5 7.1.1 setenv SUBJECTS_DIR /media/yelab/data/PD/PD_Nii/sub1/STRUC/ cd /home/yelab mri_segreg --mov /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii --init-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/bbr.pass1.dat --out-reg /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat.mincost --dof 6 --nmax 36 --param /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --wm-gt-gm 0.5 sysname Linux hostname yelab-Precision-5820-Tower machine x86_64 user yelab movvol /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/template.nii regfile /media/yelab/data/PD/PD_Nii/sub1/tmp.bbregister.6630/bbr.pass1.dat subject pd_struc_recon dof 6 outregfile /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.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 1622482081 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg 0.97067 0.00513 -0.24036 -1.30623; 0.13987 0.80110 0.58196 7.76308; 0.19554 -0.59851 0.77688 11.83703; 0.00000 0.00000 0.00000 1.00000; Loading mov Projecting LH Surfs Loading lh.white surf Loading lh.thickness for GM GM Proj: 1 0.500000 2.000000 WM Proj: 0 0.500000 2.000000 Projecting RH Surfs Loading rh.white surf Loading rh.thickness for GM Projecting RH Surfs Using lh.cortex.label Using rh.cortex.label Computing relative cost 0 -25.0 -25.0 -25.0 0.952358 1 -25.0 -25.0 25.0 0.962523 2 -25.0 25.0 -25.0 0.958242 3 -25.0 25.0 25.0 0.994533 4 25.0 -25.0 -25.0 0.957538 5 25.0 -25.0 25.0 0.965800 6 25.0 25.0 -25.0 0.954540 7 25.0 25.0 25.0 0.983962 REL: 8 0.962042 7.729495 0.966187 rel = 0.99571 Initial costs ---------------- Number of surface hits 225196 WM Intensity 25.5892 +/- 12.8831 Ctx Intensity 25.0382 +/- 13.4744 Pct Contrast -3.9798 +/- 48.9485 Cost 0.9620 RelCost 0.9957 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.8891 0.8891 0.0 1 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.8864 0.8864 0.0 2 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.8826 0.8826 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.8817 0.8817 0.0 5 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.8801 0.8801 0.0 6 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 -0.1000 0.8798 0.8798 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.8780 0.8780 0.0 354 0.0000 0.0000 0.0000 -0.1000 0.0000 -0.1000 0.8779 0.8779 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.8770 0.8770 0.0 Brute Force -------------------------- Min cost was 0.876969 Number of iterations 729 Search time 0.967691 sec Parameters at best (transmm, rotdeg) 0.000 0.000 0.000 0.000 0.000 -0.100 -------------------------------------------- Starting Powell Minimization Init Powel Params dof = 6 0 0 1 0 2 0 3 0 4 0 5 -0.1 fs_powell::minimize nparams 6 maxfev 36 ftol 0.000000 linmin_xtol_ 0.001000 powell nthiter 0: fret = 0.962285 2 1.000 0.000 0.000 0.000 0.000 -0.100 0.9611735577 6 0.618 0.000 0.000 0.000 0.000 -0.100 0.9605749283 9 0.601 0.000 0.000 0.000 0.000 -0.100 0.9605616604 12 0.608 0.000 0.000 0.000 0.000 -0.100 0.9605549512 13 0.607 0.000 0.000 0.000 0.000 -0.100 0.9605447595 16 0.607 1.000 0.000 0.000 0.000 -0.100 0.9571370086 27 0.607 1.016 0.000 0.000 0.000 -0.100 0.9571250149 33 0.607 1.016 1.000 0.000 0.000 -0.100 0.9561806481 34 0.607 1.016 2.618 0.000 0.000 -0.100 0.9526536995 35 0.607 1.016 5.236 0.000 0.000 -0.100 0.9498119955 49 0.607 1.016 5.237 0.000 0.000 -0.100 0.9498108401 59 0.607 1.016 5.237 0.052 0.000 -0.100 0.9498065454 61 0.607 1.016 5.237 0.026 0.000 -0.100 0.9497580285 67 0.607 1.016 5.237 0.026 1.000 -0.100 0.9470618800 68 0.607 1.016 5.237 0.026 2.618 -0.100 0.9433673451 75 0.607 1.016 5.237 0.026 2.761 -0.100 0.9433361345 78 0.607 1.016 5.237 0.026 2.795 -0.100 0.9433298214 79 0.607 1.016 5.237 0.026 2.816 -0.100 0.9433112137 81 0.607 1.016 5.237 0.026 2.808 -0.100 0.9432592662 84 0.607 1.016 5.237 0.026 2.809 -0.100 0.9432558428 86 0.607 1.016 5.237 0.026 2.809 0.900 0.9426233753 90 0.607 1.016 5.237 0.026 2.809 0.518 0.9422097883 91 0.607 1.016 5.237 0.026 2.809 0.282 0.9420236555 94 0.607 1.016 5.237 0.026 2.809 0.372 0.9418714007 97 0.607 1.016 5.237 0.026 2.809 0.390 0.9418329733 101 0.607 1.016 5.237 0.026 2.809 0.389 0.9418290181 powell nthiter 1: fret = 0.941829 105 -1.011 1.016 5.237 0.026 2.809 0.389 0.9394543907 106 -0.402 1.016 5.237 0.026 2.809 0.389 0.9375972401 111 -0.491 1.016 5.237 0.026 2.809 0.389 0.9375675804 113 -0.457 1.016 5.237 0.026 2.809 0.389 0.9375085190 114 -0.451 1.016 5.237 0.026 2.809 0.389 0.9374969404 115 -0.432 1.016 5.237 0.026 2.809 0.389 0.9374866069 116 -0.436 1.016 5.237 0.026 2.809 0.389 0.9374813390 119 -0.437 1.016 5.237 0.026 2.809 0.389 0.9374791653 124 -0.437 0.398 5.237 0.026 2.809 0.389 0.9353687083 126 -0.437 0.541 5.237 0.026 2.809 0.389 0.9353293773 127 -0.437 0.487 5.237 0.026 2.809 0.389 0.9351684128 128 -0.437 0.473 5.237 0.026 2.809 0.389 0.9351405092 130 -0.437 0.468 5.237 0.026 2.809 0.389 0.9350995696 134 -0.437 0.467 5.237 0.026 2.809 0.389 0.9350981613 141 -0.437 0.467 5.127 0.026 2.809 0.389 0.9350727239 142 -0.437 0.467 5.167 0.026 2.809 0.389 0.9350610980 143 -0.437 0.467 5.166 0.026 2.809 0.389 0.9350538540 146 -0.437 0.467 5.163 0.026 2.809 0.389 0.9350509917 147 -0.437 0.467 5.164 0.026 2.809 0.389 0.9350412473 155 -0.437 0.467 5.164 0.058 2.809 0.389 0.9349905808 157 -0.437 0.467 5.164 0.060 2.809 0.389 0.9349726065 158 -0.437 0.467 5.164 0.081 2.809 0.389 0.9349334490 161 -0.437 0.467 5.164 0.086 2.809 0.389 0.9349145745 166 -0.437 0.467 5.164 0.086 3.809 0.389 0.9343410526 170 -0.437 0.467 5.164 0.086 3.427 0.389 0.9336016677 172 -0.437 0.467 5.164 0.086 3.516 0.389 0.9334001827 174 -0.437 0.467 5.164 0.086 3.511 0.389 0.9333566940 176 -0.437 0.467 5.164 0.086 3.499 0.389 0.9333369642 177 -0.437 0.467 5.164 0.086 3.503 0.389 0.9333356192 189 -0.437 0.467 5.164 0.086 3.503 0.405 0.9333339589 190 -0.437 0.467 5.164 0.086 3.503 0.397 0.9333278643 193 -0.437 0.467 5.164 0.086 3.503 0.396 0.9333202959 powell nthiter 2: fret = 0.933320 207 -0.439 0.467 5.164 0.086 3.503 0.396 0.9333147152 229 -0.439 0.467 4.943 0.086 3.503 0.396 0.9327701280 230 -0.439 0.467 4.928 0.086 3.503 0.396 0.9327425187 234 -0.439 0.467 4.923 0.086 3.503 0.396 0.9327065335 238 -0.439 0.467 4.925 0.086 3.503 0.396 0.9326994942 246 -0.439 0.467 4.925 0.210 3.503 0.396 0.9323122024 262 -0.439 0.467 4.925 0.210 3.524 0.396 0.9323085490 264 -0.439 0.467 4.925 0.210 3.514 0.396 0.9322753403 278 -0.439 0.467 4.925 0.210 3.514 0.407 0.9322497034 281 -0.439 0.467 4.925 0.210 3.514 0.409 0.9322381157 powell nthiter 3: fret = 0.932238 312 -0.439 0.464 4.925 0.210 3.514 0.409 0.9322380871 328 -0.439 0.464 4.926 0.210 3.514 0.409 0.9322359446 352 -0.439 0.464 4.926 0.210 3.513 0.409 0.9322290511 powell nthiter 4: fret = 0.932229 376 -0.353 0.464 4.926 0.210 3.513 0.409 0.9322281991 379 -0.310 0.464 4.926 0.210 3.513 0.409 0.9322189836 381 -0.326 0.464 4.926 0.210 3.513 0.409 0.9322097266 382 -0.327 0.464 4.926 0.210 3.513 0.409 0.9322057831 383 -0.337 0.464 4.926 0.210 3.513 0.409 0.9321957942 385 -0.343 0.464 4.926 0.210 3.513 0.409 0.9321906653 387 -0.341 0.464 4.926 0.210 3.513 0.409 0.9321772768 400 -0.341 0.466 4.926 0.210 3.513 0.409 0.9321740261 410 -0.341 0.466 4.853 0.210 3.513 0.409 0.9321197101 415 -0.341 0.466 4.852 0.210 3.513 0.409 0.9321156290 430 -0.341 0.466 4.852 0.211 3.513 0.409 0.9321024411 444 -0.341 0.466 4.852 0.211 3.510 0.409 0.9320974247 457 -0.341 0.466 4.852 0.211 3.510 0.419 0.9320967787 459 -0.341 0.466 4.852 0.211 3.510 0.425 0.9320918695 461 -0.341 0.466 4.852 0.211 3.510 0.422 0.9320908531 462 -0.341 0.466 4.852 0.211 3.510 0.421 0.9320899924 powell nthiter 5: fret = 0.932090 475 -0.344 0.466 4.852 0.211 3.510 0.421 0.9320834295 476 -0.345 0.466 4.852 0.211 3.510 0.421 0.9320803050 478 -0.346 0.466 4.852 0.211 3.510 0.421 0.9320719408 491 -0.346 0.468 4.852 0.211 3.510 0.421 0.9320587120 493 -0.346 0.467 4.852 0.211 3.510 0.421 0.9320581806 515 -0.346 0.467 4.852 0.219 3.510 0.421 0.9320344947 powell nthiter 6: fret = 0.932034 575 -0.346 0.472 4.852 0.219 3.510 0.421 0.9320222392 577 -0.346 0.474 4.852 0.219 3.510 0.421 0.9320130723 578 -0.346 0.473 4.852 0.219 3.510 0.421 0.9320047530 590 -0.346 0.473 4.858 0.219 3.510 0.421 0.9319988496 592 -0.346 0.473 4.856 0.219 3.510 0.421 0.9319950161 593 -0.346 0.473 4.855 0.219 3.510 0.421 0.9319929912 594 -0.346 0.473 4.854 0.219 3.510 0.421 0.9319910580 powell nthiter 7: fret = 0.931991 665 -0.346 0.472 4.854 0.219 3.510 0.421 0.9319898268 powell nthiter 8: fret = 0.931990 Powell done niters = 8 Computing relative cost 0 -25.0 -25.0 -25.0 0.953742 1 -25.0 -25.0 25.0 0.973824 2 -25.0 25.0 -25.0 0.949964 3 -25.0 25.0 25.0 0.973567 4 25.0 -25.0 -25.0 0.968409 5 25.0 -25.0 25.0 0.987444 6 25.0 25.0 -25.0 0.938411 7 25.0 25.0 25.0 0.970687 REL: 8 0.931990 7.716049 0.964506 rel = 0.966287 Number of iterations 8 Min cost was 0.931990 Number of FunctionCalls 804 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 48.154961 sec Parameters at optimum (transmm) -0.34624 0.47236 4.85384 Parameters at optimum (rotdeg) 0.21859 3.51022 0.42135 Final costs ---------------- Number of surface hits 215787 WM Intensity 25.2205 +/- 11.6732 Ctx Intensity 24.4883 +/- 11.9962 Pct Contrast -4.6052 +/- 49.5418 Cost 0.9320 RelCost 0.9957 Reg at min cost was 0.97980 -0.03724 -0.19646 -0.98021; 0.14633 0.80312 0.57756 8.18577; 0.13627 -0.59465 0.79235 16.77811; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat, type = 14 Original Reg 0.97067 0.00513 -0.24036 -1.30623; 0.13987 0.80110 0.58196 7.76308; 0.19554 -0.59851 0.77688 11.83703; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00913 0.04237 -0.04390 -0.32602; -0.00646 -0.00203 0.00440 -0.42269; 0.05927 -0.00386 -0.01547 -4.94108; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 7.138636 Computing change in rh position Surface-RMS-Diff-mm 5.511752 1.966478 9.254319 mri_segreg done MinCost: 0.931990 25.220533 24.488288 -4.605166 Cleaning up Started at 2021��� 05��� 28��� ��������� 11:17:14 CST Ended at 2021��� 05��� 28��� ��������� 11:19:25 CST BBR-Run-Time-Sec 131 bbregister Done To check results, run: tkregisterfv --mov /media/yelab/data/PD/PD_Nii_withCBF/PD001/CBF/CBF.nii.gz --reg /media/yelab/data/PD/PD_Nii/sub1/register_perfusion.dat --surfs