Logfile for bbregister Sat May 22 06:44:16 UTC 2021 setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts /opt/freesurfer/bin/bbregister --s sub-01 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz --lta /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.lta --init-coreg --T2 $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux blg5521.int.ets1.calculquebec.ca 3.10.0-1160.25.1.el7.x86_64 #1 SMP Wed Apr 28 21:49:45 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer mri_convert /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii mri_convert.bin /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz... TR=3200.00, 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii... mri_coreg --s sub-01 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts cmdline mri_coreg --s sub-01 --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --regdat /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.init.dat --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask sysname Linux hostname blg5521.int.ets1.calculquebec.ca machine x86_64 user bpinsard dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii Reading in ref /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/brainmask.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.1976 0.5828 12.4553 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 4 movsat = 3372.0000 mov gstd 1.9140 1.9140 1.9140 Smoothing mov refsat = 116.0000 ref gstd 1.9140 1.9140 1.9140 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0326158343 nhits = 309410 out of 32768000, Percent Overlap: 60.4 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.19760; 0.00000 1.00000 0.00000 0.58276; 0.00000 0.00000 1.00000 12.45528; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox -1.00000 0.00000 0.00000 262.99997; 0.00000 0.00000 1.00000 -9.99998; 0.00000 -1.00000 0.00000 318.99994; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -0.19760 -5.41724 2.45528 2.00000 0.00000 0.00000 -1.0313521 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0343925953 #@# 4 188 -0.19760 -5.41724 2.45528 2.00000 0.00000 0.00000 -1.0343926 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.034393 #@# 4 194 0.18436 -5.41724 2.45528 2.00000 0.00000 0.00000 -1.0344205 #@# 4 196 0.22881 -5.41724 2.45528 2.00000 0.00000 0.00000 -1.0344213 #@# 4 200 0.22881 -4.41724 2.45528 2.00000 0.00000 0.00000 -1.0351841 #@# 4 201 0.22881 -2.79921 2.45528 2.00000 0.00000 0.00000 -1.0364153 #@# 4 207 0.22881 0.61053 2.45528 2.00000 0.00000 0.00000 -1.0367589 #@# 4 208 0.22881 -0.61227 2.45528 2.00000 0.00000 0.00000 -1.0372336 #@# 4 210 0.22881 -0.73017 2.45528 2.00000 0.00000 0.00000 -1.0372372 #@# 4 217 0.22881 -0.72017 1.83725 2.00000 0.00000 0.00000 -1.0373724 #@# 4 218 0.22881 -0.72017 1.45528 2.00000 0.00000 0.00000 -1.0373764 #@# 4 219 0.22881 -0.72017 1.62077 2.00000 0.00000 0.00000 -1.0373833 #@# 4 220 0.22881 -0.72017 1.63077 2.00000 0.00000 0.00000 -1.0373834 #@# 4 225 0.22881 -0.72017 1.64225 0.38197 0.00000 0.00000 -1.0377817 #@# 4 229 0.22881 -0.72017 1.64225 0.61803 0.00000 0.00000 -1.0378000 #@# 4 230 0.22881 -0.72017 1.64225 0.63623 0.00000 0.00000 -1.0378001 #@# 4 251 0.22881 -0.72017 1.64225 0.65623 0.00000 -0.07449 -1.0378014 powell nthiter 1: fret = -1.037801 #@# 4 264 0.14019 -0.72017 1.64225 0.65623 0.00000 -0.08449 -1.0378045 #@# 4 272 0.15426 -0.33821 1.64225 0.65623 0.00000 -0.08449 -1.0378433 #@# 4 273 0.15426 -0.37545 1.64225 0.65623 0.00000 -0.08449 -1.0378443 #@# 4 274 0.15426 -0.39149 1.64225 0.65623 0.00000 -0.08449 -1.0378444 #@# 4 281 0.15426 -0.40149 1.02421 0.65623 0.00000 -0.08449 -1.0378937 #@# 4 283 0.15426 -0.40149 1.19648 0.65623 0.00000 -0.08449 -1.0379030 #@# 4 284 0.15426 -0.40149 1.20648 0.65623 0.00000 -0.08449 -1.0379031 #@# 4 285 0.15426 -0.40149 1.22731 0.65623 0.00000 -0.08449 -1.0379032 #@# 4 293 0.15426 -0.40149 1.21731 0.03819 0.00000 -0.08449 -1.0379069 #@# 4 295 0.15426 -0.40149 1.21731 0.33736 0.00000 -0.08449 -1.0379328 #@# 4 304 0.15426 -0.40149 1.21731 0.33736 0.06855 -0.08449 -1.0379335 #@# 4 308 0.15426 -0.40149 1.21731 0.33736 0.08181 -0.08449 -1.0379336 #@# 4 318 0.07971 -0.08280 0.79237 0.01849 0.16362 -0.05245 -1.0379341 powell nthiter 2: fret = -1.037934 #@# 4 325 0.10335 -0.40149 1.21731 0.33736 0.08181 -0.06847 -1.0379355 #@# 4 326 0.09335 -0.40149 1.21731 0.33736 0.08181 -0.06847 -1.0379360 #@# 4 337 0.09335 -0.28468 1.21731 0.33736 0.08181 -0.06847 -1.0379429 #@# 4 349 0.09335 -0.26468 1.08628 0.33736 0.08181 -0.06847 -1.0379483 #@# 4 360 0.09335 -0.26468 1.06642 0.23075 0.08181 -0.06847 -1.0379521 #@# 4 370 0.09335 -0.26468 1.06642 0.22075 0.12766 -0.06847 -1.0379522 Powell done niters total = 2 OptTimeSec 13.2 sec OptTimeMin 0.22 min nEvals 384 Final parameters 0.09334619 -0.26467815 1.06641722 0.22074908 0.12765823 -0.04256488 Final cost -1.037952241013345 --------------------------------- mri_coreg utimesec 207.681360 mri_coreg stimesec 1.032778 mri_coreg ru_maxrss 890680 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 897370 mri_coreg ru_majflt 2 mri_coreg ru_nswap 0 mri_coreg ru_inblock 10744 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 928 mri_coreg ru_nivcsw 106 Final RefRAS-to-MovRAS 1.00000 -0.00074 0.00223 0.09335; 0.00073 0.99999 0.00385 -0.26468; -0.00223 -0.00385 0.99999 1.06642; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox -1.00000 -0.00223 -0.00074 263.80264; -0.00073 -0.00385 0.99999 -10.33881; 0.00223 -0.99999 -0.00385 304.87857; 0.00000 0.00000 0.00000 1.00000; Final parameters 0.0933 -0.2647 1.0664 0.2207 0.1277 -0.0426 nhits = 294522 out of 32768000, Percent Overlap: 57.5 mri_coreg RunTimeSec 79.1 sec To check run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --targ /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/brainmask.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/mri_coreg.lta --s sub-01 --surfs mri_coreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.init.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/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 blg5521.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.init.dat subject sub-01 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/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 1621810959 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -1.00000 0.00074 -0.00223 0.53783; -0.00223 -0.00385 0.99999 -12.30324; -0.00073 -0.99999 -0.00385 0.85922; 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 0.996595 1 -25.0 -25.0 25.0 0.927841 2 -25.0 25.0 -25.0 0.959765 3 -25.0 25.0 25.0 0.982920 4 25.0 -25.0 -25.0 0.980832 5 25.0 -25.0 25.0 0.955574 6 25.0 25.0 -25.0 0.967909 7 25.0 25.0 25.0 0.965003 REL: 8 0.214908 7.736438 0.967055 rel = 0.222229 Initial costs ---------------- Number of surface hits 4521 WM Intensity 809.1536 +/- 248.4808 Ctx Intensity 1054.3440 +/- 290.5009 Pct Contrast 26.7938 +/- 21.7071 Cost 0.2149 RelCost 0.2222 ------------------------------------ Brute force preopt -4 4 4, n = 729 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 0.9398 0.9398 0.0 6 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 -4.0000 0.9035 0.9035 0.0 7 -4.0000 -4.0000 -4.0000 -4.0000 4.0000 0.0000 0.9024 0.9024 0.0 15 -4.0000 -4.0000 -4.0000 0.0000 4.0000 -4.0000 0.8211 0.8211 0.0 39 -4.0000 -4.0000 0.0000 0.0000 0.0000 -4.0000 0.7875 0.7875 0.0 102 -4.0000 0.0000 -4.0000 4.0000 0.0000 -4.0000 0.7795 0.7795 0.0 120 -4.0000 0.0000 0.0000 0.0000 0.0000 -4.0000 0.6999 0.6999 0.0 274 0.0000 -4.0000 0.0000 -4.0000 0.0000 0.0000 0.6990 0.6990 0.0 346 0.0000 0.0000 -4.0000 4.0000 0.0000 0.0000 0.6267 0.6267 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.2149 0.2149 0.0 Brute Force -------------------------- Min cost was 0.214908 Number of iterations 729 Search time 1.969000 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 = 0.214908 8 -0.010 0.000 0.000 0.000 0.000 0.000 0.2148273770 11 -0.044 0.000 0.000 0.000 0.000 0.000 0.2143858944 15 -0.042 0.000 0.000 0.000 0.000 0.000 0.2143845147 19 -0.042 -1.618 0.000 0.000 0.000 0.000 0.1244587402 20 -0.042 -1.185 0.000 0.000 0.000 0.000 0.0905543981 24 -0.042 -1.171 0.000 0.000 0.000 0.000 0.0903606841 25 -0.042 -1.139 0.000 0.000 0.000 0.000 0.0900749272 31 -0.042 -1.137 0.000 0.000 0.000 0.000 0.0900744979 39 -0.042 -1.137 -0.053 0.000 0.000 0.000 0.0887745006 40 -0.042 -1.137 -0.209 0.000 0.000 0.000 0.0881101435 42 -0.042 -1.137 -0.153 0.000 0.000 0.000 0.0881019729 44 -0.042 -1.137 -0.114 0.000 0.000 0.000 0.0878955931 47 -0.042 -1.137 -0.116 0.000 0.000 0.000 0.0878936890 55 -0.042 -1.137 -0.116 0.179 0.000 0.000 0.0825719606 58 -0.042 -1.137 -0.116 0.167 0.000 0.000 0.0824795693 67 -0.042 -1.137 -0.116 0.167 -0.032 0.000 0.0812389110 69 -0.042 -1.137 -0.116 0.167 -0.122 0.000 0.0800331275 72 -0.042 -1.137 -0.116 0.167 -0.118 0.000 0.0800224930 82 -0.042 -1.137 -0.116 0.167 -0.118 -0.019 0.0795838400 84 -0.042 -1.137 -0.116 0.167 -0.118 -0.091 0.0789831517 85 -0.042 -1.137 -0.116 0.167 -0.118 -0.082 0.0789180387 86 -0.042 -1.137 -0.116 0.167 -0.118 -0.072 0.0788812625 88 -0.042 -1.137 -0.116 0.167 -0.118 -0.070 0.0788792023 89 -0.042 -1.137 -0.116 0.167 -0.118 -0.069 0.0788786295 92 -0.042 -1.137 -0.116 0.167 -0.118 -0.068 0.0788786011 powell nthiter 1: fret = 0.078879 100 -0.011 -1.137 -0.116 0.167 -0.118 -0.068 0.0781527653 102 0.006 -1.137 -0.116 0.167 -0.118 -0.068 0.0779238729 103 0.011 -1.137 -0.116 0.167 -0.118 -0.068 0.0779184134 104 0.010 -1.137 -0.116 0.167 -0.118 -0.068 0.0779176983 112 0.010 -1.085 -0.116 0.167 -0.118 -0.068 0.0775754813 113 0.010 -1.089 -0.116 0.167 -0.118 -0.068 0.0775470536 114 0.010 -1.101 -0.116 0.167 -0.118 -0.068 0.0774715114 115 0.010 -1.115 -0.116 0.167 -0.118 -0.068 0.0774687427 116 0.010 -1.108 -0.116 0.167 -0.118 -0.068 0.0774565651 118 0.010 -1.110 -0.116 0.167 -0.118 -0.068 0.0774557632 126 0.010 -1.110 -0.141 0.167 -0.118 -0.068 0.0770488771 128 0.010 -1.110 -0.167 0.167 -0.118 -0.068 0.0768253815 129 0.010 -1.110 -0.168 0.167 -0.118 -0.068 0.0768236424 130 0.010 -1.110 -0.169 0.167 -0.118 -0.068 0.0768235732 138 0.010 -1.110 -0.169 0.207 -0.118 -0.068 0.0759564035 140 0.010 -1.110 -0.169 0.221 -0.118 -0.068 0.0759111315 141 0.010 -1.110 -0.169 0.220 -0.118 -0.068 0.0759107940 152 0.010 -1.110 -0.169 0.220 -0.137 -0.068 0.0758761123 155 0.010 -1.110 -0.169 0.220 -0.140 -0.068 0.0758663251 156 0.010 -1.110 -0.169 0.220 -0.144 -0.068 0.0758656674 158 0.010 -1.110 -0.169 0.220 -0.143 -0.068 0.0758648239 168 0.010 -1.110 -0.169 0.220 -0.143 -0.067 0.0758635106 169 0.010 -1.110 -0.169 0.220 -0.143 -0.061 0.0758591525 171 0.010 -1.110 -0.169 0.220 -0.143 -0.059 0.0758579389 173 0.010 -1.110 -0.169 0.220 -0.143 -0.060 0.0758579061 powell nthiter 2: fret = 0.075858 182 0.047 -1.110 -0.169 0.220 -0.143 -0.060 0.0755910157 183 0.046 -1.110 -0.169 0.220 -0.143 -0.060 0.0755909128 191 0.046 -1.063 -0.169 0.220 -0.143 -0.060 0.0750137982 193 0.046 -1.068 -0.169 0.220 -0.143 -0.060 0.0750120593 194 0.046 -1.066 -0.169 0.220 -0.143 -0.060 0.0750106787 195 0.046 -1.067 -0.169 0.220 -0.143 -0.060 0.0750106713 202 0.046 -1.067 -0.173 0.220 -0.143 -0.060 0.0749510095 204 0.046 -1.067 -0.203 0.220 -0.143 -0.060 0.0749107861 205 0.046 -1.067 -0.189 0.220 -0.143 -0.060 0.0748112318 207 0.046 -1.067 -0.190 0.220 -0.143 -0.060 0.0748110542 216 0.046 -1.067 -0.190 0.227 -0.143 -0.060 0.0748053226 217 0.046 -1.067 -0.190 0.226 -0.143 -0.060 0.0748021092 218 0.046 -1.067 -0.190 0.224 -0.143 -0.060 0.0748010223 240 0.046 -1.067 -0.190 0.224 -0.143 -0.034 0.0747388655 241 0.046 -1.067 -0.190 0.224 -0.143 -0.033 0.0747386853 242 0.046 -1.067 -0.190 0.224 -0.143 -0.032 0.0747384717 powell nthiter 3: fret = 0.074738 256 0.044 -1.067 -0.190 0.224 -0.143 -0.032 0.0747359631 266 0.044 -1.066 -0.190 0.224 -0.143 -0.032 0.0747291681 267 0.044 -1.059 -0.190 0.224 -0.143 -0.032 0.0747210009 269 0.044 -1.061 -0.190 0.224 -0.143 -0.032 0.0747164637 291 0.044 -1.061 -0.190 0.223 -0.143 -0.032 0.0747154511 312 0.044 -1.061 -0.190 0.223 -0.143 -0.031 0.0747145722 314 0.044 -1.061 -0.190 0.223 -0.143 -0.029 0.0747138140 powell nthiter 4: fret = 0.074714 325 0.043 -1.061 -0.190 0.223 -0.143 -0.029 0.0747132007 Powell done niters = 4 Computing relative cost 0 -25.0 -25.0 -25.0 0.988856 1 -25.0 -25.0 25.0 0.929248 2 -25.0 25.0 -25.0 0.944263 3 -25.0 25.0 25.0 0.989870 4 25.0 -25.0 -25.0 0.964532 5 25.0 -25.0 25.0 0.962769 6 25.0 25.0 -25.0 0.964406 7 25.0 25.0 25.0 0.960109 REL: 8 0.074713 7.704054 0.963007 rel = 0.0775833 Number of iterations 4 Min cost was 0.074713 Number of FunctionCalls 378 TolPowell 0.000100 nMaxItersPowell 36 OptimizationTime 0.859000 sec Parameters at optimum (transmm) 0.04283 -1.06131 -0.19044 Parameters at optimum (rotdeg) 0.22281 -0.14267 -0.02944 Final costs ---------------- Number of surface hits 4521 WM Intensity 789.3921 +/- 233.2047 Ctx Intensity 1035.2156 +/- 249.7474 Pct Contrast 28.0767 +/- 15.7256 Cost 0.0747 RelCost 0.2222 Reg at min cost was -0.99999 0.00323 -0.00171 0.57231; -0.00171 0.00004 1.00000 -13.36807; -0.00323 -0.99999 0.00003 0.62226; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/bbr.pass1.dat, type = 14 Original Reg -1.00000 0.00074 -0.00223 0.53783; -0.00223 -0.00385 0.99999 -12.30324; -0.00073 -0.99999 -0.00385 0.85922; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg -0.00000 -0.00249 -0.00051 -0.03449; -0.00052 -0.00389 -0.00001 1.06484; 0.00250 0.00000 -0.00388 0.23696; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 1.174637 Computing change in rh position Surface-RMS-Diff-mm 1.154589 0.154894 1.483860 mri_segreg done mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 $Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $ setenv SUBJECTS_DIR /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer cd /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/scripts mri_segreg --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii --init-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/bbr.pass1.dat --out-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 sysname Linux hostname blg5521.int.ets1.calculquebec.ca machine x86_64 user bpinsard movvol /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/template.nii regfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/tmp.bbregister.119755/bbr.pass1.dat subject sub-01 dof 6 outregfile /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.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 1621808495 TransRandMax 0.000000 RotRandMax 0.000000 Translations 0.000000 0.000000 0.000000 Rotations 0.000000 0.000000 0.000000 Input reg -0.99999 0.00323 -0.00171 0.57231; -0.00171 0.00004 1.00000 -13.36807; -0.00323 -0.99999 0.00003 0.62226; 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 0.987537 1 -25.0 -25.0 25.0 0.959314 2 -25.0 25.0 -25.0 0.952374 3 -25.0 25.0 25.0 0.974839 4 25.0 -25.0 -25.0 0.976526 5 25.0 -25.0 25.0 0.961975 6 25.0 25.0 -25.0 0.977409 7 25.0 25.0 25.0 0.962467 REL: 8 0.079543 7.752442 0.969055 rel = 0.0820835 Initial costs ---------------- Number of surface hits 450857 WM Intensity 792.5982 +/- 235.5551 Ctx Intensity 1038.8829 +/- 249.5455 Pct Contrast 28.1030 +/- 15.7312 Cost 0.0795 RelCost 0.0821 ------------------------------------ Brute force preopt -0.1 0.1 0.1, n = 729 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 0.0882 0.0882 0.0 3 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 -0.1000 0.0852 0.0852 0.0 4 -0.1000 -0.1000 -0.1000 -0.1000 0.0000 0.0000 0.0834 0.0834 0.0 7 -0.1000 -0.1000 -0.1000 -0.1000 0.1000 0.0000 0.0829 0.0829 0.0 15 -0.1000 -0.1000 -0.1000 0.0000 0.1000 -0.1000 0.0824 0.0824 0.0 16 -0.1000 -0.1000 -0.1000 0.0000 0.1000 0.0000 0.0818 0.0818 0.0 31 -0.1000 -0.1000 0.0000 -0.1000 0.0000 0.0000 0.0815 0.0815 0.0 39 -0.1000 -0.1000 0.0000 0.0000 0.0000 -0.1000 0.0795 0.0795 0.0 97 -0.1000 0.0000 -0.1000 0.0000 0.1000 0.0000 0.0789 0.0789 0.0 120 -0.1000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0766 0.0766 0.0 363 0.0000 0.0000 0.0000 0.0000 0.0000 -0.1000 0.0755 0.0755 0.0 364 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0747 0.0747 0.0 Brute Force -------------------------- Min cost was 0.074713 Number of iterations 729 Search time 1.605000 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 = 0.079543 7 0.010 0.000 0.000 0.000 0.000 0.000 0.0795222644 8 0.014 0.000 0.000 0.000 0.000 0.000 0.0795194104 17 0.014 0.059 0.000 0.000 0.000 0.000 0.0790564248 18 0.014 0.060 0.000 0.000 0.000 0.000 0.0790559307 27 0.014 0.060 0.013 0.000 0.000 0.000 0.0790483838 30 0.014 0.060 0.012 0.000 0.000 0.000 0.0790483815 37 0.014 0.060 0.012 0.021 0.000 0.000 0.0790290504 38 0.014 0.060 0.012 0.013 0.000 0.000 0.0790172436 39 0.014 0.060 0.012 0.012 0.000 0.000 0.0790171203 47 0.014 0.060 0.012 0.012 0.090 0.000 0.0781049037 48 0.014 0.060 0.012 0.012 0.083 0.000 0.0780996430 50 0.014 0.060 0.012 0.012 0.082 0.000 0.0780995287 61 0.014 0.060 0.012 0.012 0.082 0.083 0.0775087818 63 0.014 0.060 0.012 0.012 0.082 0.078 0.0775061110 64 0.014 0.060 0.012 0.012 0.082 0.077 0.0775060543 powell nthiter 1: fret = 0.077506 74 0.013 0.060 0.012 0.012 0.082 0.077 0.0775060221 83 0.013 0.054 0.012 0.012 0.082 0.077 0.0775032596 84 0.013 0.055 0.012 0.012 0.082 0.077 0.0775030791 93 0.013 0.055 -0.000 0.012 0.082 0.077 0.0774752958 96 0.013 0.055 -0.006 0.012 0.082 0.077 0.0774711972 114 0.013 0.055 -0.006 0.012 0.103 0.077 0.0774578258 115 0.013 0.055 -0.006 0.012 0.094 0.077 0.0774519479 116 0.013 0.055 -0.006 0.012 0.095 0.077 0.0774519443 117 0.013 0.055 -0.006 0.012 0.096 0.077 0.0774517760 127 0.013 0.055 -0.006 0.012 0.096 0.080 0.0774506671 128 0.013 0.055 -0.006 0.012 0.096 0.081 0.0774504426 powell nthiter 2: fret = 0.077450 138 0.010 0.055 -0.006 0.012 0.096 0.081 0.0774503801 140 0.011 0.055 -0.006 0.012 0.096 0.081 0.0774501605 148 0.011 0.052 -0.006 0.012 0.096 0.081 0.0774499611 150 0.011 0.053 -0.006 0.012 0.096 0.081 0.0774496869 160 0.011 0.053 -0.008 0.012 0.096 0.081 0.0774492785 161 0.011 0.053 -0.007 0.012 0.096 0.081 0.0774492672 169 0.011 0.053 -0.007 0.010 0.096 0.081 0.0774487377 178 0.011 0.053 -0.007 0.010 0.098 0.081 0.0774486981 179 0.011 0.053 -0.007 0.010 0.099 0.081 0.0774485549 191 0.011 0.053 -0.007 0.010 0.099 0.080 0.0774484888 powell nthiter 3: fret = 0.077448 202 0.010 0.053 -0.007 0.010 0.099 0.080 0.0774484577 221 0.010 0.053 -0.006 0.010 0.099 0.080 0.0774484293 248 0.010 0.053 -0.006 0.010 0.099 0.079 0.0774483571 powell nthiter 4: fret = 0.077448 304 0.010 0.053 -0.006 0.010 0.099 0.080 0.0774482633 powell nthiter 5: fret = 0.077448 Powell done niters = 5 Computing relative cost 0 -25.0 -25.0 -25.0 0.989084 1 -25.0 -25.0 25.0 0.958923 2 -25.0 25.0 -25.0 0.951135 3 -25.0 25.0 25.0 0.974614 4 25.0 -25.0 -25.0 0.975537 5 25.0 -25.0 25.0 0.961659 6 25.0 25.0 -25.0 0.977388 7 25.0 25.0 25.0 0.963059 REL: 8 0.077448 7.751399 0.968925 rel = 0.0799322 Number of iterations 5 Min cost was 0.077448 Number of FunctionCalls 362 TolPowell 0.000000 nMaxItersPowell 36 OptimizationTime 42.688000 sec Parameters at optimum (transmm) 0.01013 0.05307 -0.00640 Parameters at optimum (rotdeg) 0.01040 0.09853 0.07955 Final costs ---------------- Number of surface hits 450857 WM Intensity 792.9120 +/- 235.6028 Ctx Intensity 1039.0331 +/- 249.1212 Pct Contrast 28.0834 +/- 15.6924 Cost 0.0774 RelCost 0.0821 Reg at min cost was -0.99999 0.00151 -0.00310 0.60207; -0.00310 0.00022 0.99999 -13.31431; -0.00151 -1.00000 0.00021 0.61245; 0.00000 0.00000 0.00000 1.00000; Writing optimal reg to /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat, type = 14 Original Reg -0.99999 0.00323 -0.00171 0.57231; -0.00171 0.00004 1.00000 -13.36807; -0.00323 -0.99999 0.00003 0.62226; 0.00000 0.00000 0.00000 1.00000; Original Reg - Optimal Reg 0.00000 0.00172 0.00139 -0.02975; 0.00139 -0.00018 0.00000 -0.05377; -0.00172 0.00000 -0.00018 0.00981; 0.00000 0.00000 0.00000 0.00000; Computing change in lh position LH rmsDiffMean 0.133675 Computing change in rh position Surface-RMS-Diff-mm 0.113053 0.039601 0.214832 mri_segreg done MinCost: 0.077448 792.911998 1039.033057 28.083446 tkregister2_cmdl --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat --noedit --ltaout /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.lta tkregister_tcl /opt/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz reg file /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.99999 0.00151 -0.00310 0.60207; -0.00310 0.00022 0.99999 -13.31431; -0.00151 -1.00000 0.00021 0.61245; 0.00000 0.00000 0.00000 1.00000; float2int = 0 --------------------------------------- INFO: loading target /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.00000 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 /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz Tmov: -------------------- -0.80000 0.00000 0.00000 83.20000; 0.00000 0.00000 0.80000 -128.00000; 0.00000 -0.80000 0.00000 120.00000; 0.00000 0.00000 0.00000 1.00000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.99999 0.00151 -0.00310 0.60207; -0.00310 0.00022 1.00000 -13.31431; -0.00151 -1.00000 0.00021 0.61245; 0.00000 0.00000 0.00000 1.00000; Determinant -1 subject = sub-01 RegMat --------------------------- -0.99999 0.00151 -0.00310 0.60207; -0.00310 0.00022 1.00000 -13.31431; -0.00151 -1.00000 0.00021 0.61245; 0.00000 0.00000 0.00000 1.00000; Cleaning up Started at Sat May 22 06:44:16 UTC 2021 Ended at Sat May 22 06:46:48 UTC 2021 BBR-Run-Time-Sec 152 bbregister Done To check results, run: tkregisterfv --mov /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/orig/T2raw.mgz --reg /lustre03/project/6003287/datasets/cneuromod_processed/smriprep/sourcedata/freesurfer/sub-01/mri/transforms/T2raw.auto.lta --surfs