Hi Douglas, I have just sent it to you on Filedrop.
Best regards, Matthieu 2016-10-03 17:45 GMT+02:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > Can you tar up the FS anat analysis and BS7_PET.lps.nii.gz and send it to > me on our filedrop? > > On 10/3/16 6:55 AM, Matthieu Vanhoutte wrote: > > Hi Douglas, > > Please find below the mri_coreg terminal output : > > *$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $* > *cwd /NAS/tupac/matthieu/FS5.3/207118_M0_2014-01-29/pet* > *cmdline mri_coreg --s 207118_M0_2014-01-29 --mov BS7_PET.lps.nii.gz --reg > Pet2T1.BS7.register.dof6.mri_coreg.lta --regdat > Pet2T1.BS7.register.dof6.mri_coreg.dat * > *sysname Linux* > *hostname yakuza* > *machine x86_64* > *user matthieu* > *dof 6* > *nsep 2* > *cras0 1* > *ftol 0.000000* > *linmintol 0.001000* > *bf 1* > *bflim 30.000000* > *bfnsamp 30* > *SmoothRef 0* > *SatPct 99.990000* > *MovOOB 0* > *optschema 1* > *Reading in mov BS7_PET.lps.nii.gz* > *Reading in ref > /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz* > *Reading in and applying refmask > /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/aparc+aseg.mgz* > *Setting cras translation parameters to align centers* > *Creating random numbers for coordinate dithering* > *Performing intensity dithering* > *Initial parameters 20.9141 11.8161 149.1538 0.0000 0.0000 0.0000 > 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 * > *Separation list (2): 4 2 min = 2* > *DoSmoothing 1* > *DoCoordDither 1* > *DoIntensityDither 1* > *nitersmax 4* > *ftol 1.000e-07* > *linmintol 1.000e-03* > *SatPct 99.990000* > *Hist FWHM 7.000000 7.000000* > *nthreads 1* > *movsat = 10897.7666* > *mov gstd 0.8459 0.8459 0.8459* > *Smoothing mov* > *refsat = 119.0000* > *ref gstd 0.8459 0.8459 0.8459* > *Smoothing ref* > *COREGpreproc() done* > *Testing if mov and target overlap* > *Init cost -1.0011578057* > *nhits = 262144 out of 16777216, Percent Overlap: 100.0* > *Initial RefRAS-to-MovRAS* > * 1.00000 0.00000 0.00000 20.91408;* > * 0.00000 1.00000 0.00000 11.81612;* > * 0.00000 0.00000 1.00000 149.15384;* > * 0.00000 0.00000 0.00000 1.00000;* > *Initial RefVox-to-MovVox* > * 1.00000 0.00000 0.00000 0.00000;* > * 0.00000 0.00000 -1.00000 255.00000;* > * 0.00000 -1.00000 0.00000 255.00000;* > * 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 4.91408 21.81612 119.15384 > 2.00000 0.00000 0.00000 -1.0078773* > *Turning MovOOB back off after brute force search* > > > *---------------------------------* > *Init Powel Params dof = 6* > *Starting OpenPowel2(), sep = 4* > *InitialCost -1.0076701641 * > *#@# 4 188 4.91408 21.81612 119.15384 2.00000 0.00000 0.00000 > -1.0076702* > *fs_powell::minimize* > * nparams 6* > * maxfev 4* > * ftol 0.000000* > * linmin_xtol_ 0.001000* > * powell nthiter 0: fret = -1.007670* > *#@# 4 197 4.93866 21.81612 119.15384 2.00000 0.00000 0.00000 > -1.0076704* > *#@# 4 198 4.96905 21.81612 119.15384 2.00000 0.00000 0.00000 > -1.0076705* > *#@# 4 209 4.97536 20.19808 119.15384 2.00000 0.00000 0.00000 > -1.0077189* > *#@# 4 210 4.97536 19.55424 119.15384 2.00000 0.00000 0.00000 > -1.0077529* > *#@# 4 211 4.97536 18.51247 119.15384 2.00000 0.00000 0.00000 > -1.0078081* > *#@# 4 212 4.97536 16.82685 119.15384 2.00000 0.00000 0.00000 > -1.0078434* > *#@# 4 213 4.97536 16.77889 119.15384 2.00000 0.00000 0.00000 > -1.0078460* > *#@# 4 214 4.97536 16.70129 119.15384 2.00000 0.00000 0.00000 > -1.0078515* > *#@# 4 215 4.97536 16.57572 119.15384 2.00000 0.00000 0.00000 > -1.0078617* > *#@# 4 216 4.97536 16.37254 119.15384 2.00000 0.00000 0.00000 > -1.0078768* > *#@# 4 217 4.97536 14.89926 119.15384 2.00000 0.00000 0.00000 > -1.0079292* > *#@# 4 218 4.97536 14.85724 119.15384 2.00000 0.00000 0.00000 > -1.0079303* > *#@# 4 219 4.97536 12.95773 119.15384 2.00000 0.00000 0.00000 > -1.0079467* > *#@# 4 220 4.97536 13.40911 119.15384 2.00000 0.00000 0.00000 > -1.0079498* > *#@# 4 223 4.97536 13.62039 119.15384 2.00000 0.00000 0.00000 > -1.0079516* > *#@# 4 229 4.97536 13.61634 117.53580 2.00000 0.00000 0.00000 > -1.0086172* > *#@# 4 230 4.97536 13.61634 80.23408 2.00000 0.00000 0.00000 > -1.0266197* > *#@# 4 235 4.97536 13.61634 69.09492 2.00000 0.00000 0.00000 > -1.0285894* > *#@# 4 236 4.97536 13.61634 69.00322 2.00000 0.00000 0.00000 > -1.0285913* > *#@# 4 237 4.97536 13.61634 68.30045 2.00000 0.00000 0.00000 > -1.0285933* > *#@# 4 239 4.97536 13.61634 68.58790 2.00000 0.00000 0.00000 > -1.0285972* > *#@# 4 241 4.97536 13.61634 68.56419 2.00000 0.00000 0.00000 > -1.0285974* > *#@# 4 244 4.97536 13.61634 68.54494 2.00000 0.00000 0.00000 > -1.0285981* > *#@# 4 250 4.97536 13.61634 68.54494 3.00000 0.00000 0.00000 > -1.0286810* > *#@# 4 251 4.97536 13.61634 68.54494 4.61803 0.00000 0.00000 > -1.0287892* > *#@# 4 255 4.97536 13.61634 68.54494 5.29042 0.00000 0.00000 > -1.0287902* > *#@# 4 256 4.97536 13.61634 68.54494 5.02220 0.00000 0.00000 > -1.0287969* > *#@# 4 266 4.97536 13.61634 68.54494 5.02421 1.00000 0.00000 > -1.0288255* > *#@# 4 272 4.97536 13.61634 68.54494 5.02421 1.14711 0.00000 > -1.0288261* > *#@# 4 275 4.97536 13.61634 68.54494 5.02421 1.09092 0.00000 > -1.0288264* > *#@# 4 287 4.97536 13.61634 68.54494 5.02421 1.03666 1.00000 > -1.0288312* > *#@# 4 291 4.97536 13.61634 68.54494 5.02421 1.03666 0.61803 > -1.0288329* > *#@# 4 296 4.97536 13.61634 68.54494 5.02421 1.03666 0.72161 > -1.0288330* > *#@# 4 297 4.97536 13.61634 68.54494 5.02421 1.03666 0.75100 > -1.0288332* > *#@# 4 305 4.97536 13.61634 68.54494 5.02421 1.03666 0.74092 > -1.0288333* > *#@# 4 315 4.97542 13.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288336* > * powell nthiter 1: fret = -1.028834* > *#@# 4 319 3.35739 13.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288464* > *#@# 4 320 4.02089 13.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288594* > *#@# 4 324 3.97462 13.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288596* > *#@# 4 327 4.00121 13.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288597* > *#@# 4 336 3.99013 14.60814 68.49433 5.02724 1.03770 0.74166 > -1.0288848* > *#@# 4 341 3.99013 14.70860 68.49433 5.02724 1.03770 0.74166 > -1.0288850* > *#@# 4 342 3.99013 14.68519 68.49433 5.02724 1.03770 0.74166 > -1.0288851* > *#@# 4 356 3.99013 14.67684 68.49433 5.02724 1.03770 0.70149 > -1.0288855* > *#@# 4 365 3.99013 14.67684 68.49433 6.02724 1.03770 0.68860 > -1.0288972* > *#@# 4 384 3.99013 14.67684 68.49433 6.02724 1.06723 0.68860 > -1.0288974* > *#@# 4 385 3.99013 14.67684 68.49433 6.02724 1.13709 0.68860 > -1.0288981* > *#@# 4 386 3.99013 14.67684 68.49433 6.02724 1.24502 0.68860 > -1.0288985* > *#@# 4 391 3.99013 14.67684 68.49433 6.02724 1.25019 0.68860 > -1.0288986* > *#@# 4 402 3.99037 14.64484 68.29682 6.03904 1.25424 0.69150 > -1.0289003* > *#@# 4 404 3.99030 14.65511 68.36022 6.03525 1.25294 0.69057 > -1.0289006* > * powell nthiter 2: fret = -1.028901* > *#@# 4 413 3.80284 14.65511 68.36022 6.03525 1.25294 0.69057 > -1.0289013* > *#@# 4 415 3.82815 14.65511 68.36022 6.03525 1.25294 0.69057 > -1.0289015* > *#@# 4 422 3.82147 15.65511 68.36022 6.03525 1.25294 0.69057 > -1.0289214* > *#@# 4 426 3.82147 15.27315 68.36022 6.03525 1.25294 0.69057 > -1.0289227* > *#@# 4 427 3.82147 15.40752 68.36022 6.03525 1.25294 0.69057 > -1.0289237* > *#@# 4 441 3.82147 15.39508 68.36022 6.03525 1.25294 0.44847 > -1.0289254* > *#@# 4 443 3.82147 15.39508 68.36022 6.03525 1.25294 0.30487 > -1.0289257* > *#@# 4 446 3.82147 15.39508 68.36022 6.03525 1.25294 0.32211 > -1.0289260* > *#@# 4 457 3.82147 15.39508 68.36022 6.19153 1.25294 0.32011 > -1.0289278* > *#@# 4 461 3.82147 15.39508 68.36022 6.18538 1.25294 0.32011 > -1.0289279* > *#@# 4 469 3.82147 15.39508 68.36022 6.18638 0.63491 0.32011 > -1.0289334* > *#@# 4 470 3.82147 15.39508 68.36022 6.18638 0.25294 0.32011 > -1.0289339* > *#@# 4 475 3.82147 15.39508 68.36022 6.18638 0.21850 0.32011 > -1.0289340* > *#@# 4 476 3.82147 15.39508 68.36022 6.18638 0.19721 0.32011 > -1.0289341* > *#@# 4 480 3.82147 15.39508 68.36022 6.18638 0.20785 0.32011 > -1.0289342* > *#@# 4 494 3.82131 15.41560 68.48689 6.17881 0.21339 0.31825 > -1.0289359* > * powell nthiter 3: fret = -1.028936* > *#@# 4 503 3.20328 15.41560 68.48689 6.17881 0.21339 0.31825 > -1.0289463* > *#@# 4 505 3.36275 15.41560 68.48689 6.17881 0.21339 0.31825 > -1.0289472* > *#@# 4 508 3.28979 15.41560 68.48689 6.17881 0.21339 0.31825 > -1.0289474* > *#@# 4 510 3.31021 15.41560 68.48689 6.17881 0.21339 0.31825 > -1.0289475* > *#@# 4 518 3.31196 15.79757 68.48689 6.17881 0.21339 0.31825 > -1.0289484* > *#@# 4 519 3.31196 15.62773 68.48689 6.17881 0.21339 0.31825 > -1.0289508* > *#@# 4 527 3.31196 15.62417 68.48689 6.17881 0.21339 -0.29978 > -1.0289558* > *#@# 4 529 3.31196 15.62417 68.48689 6.17881 0.21339 -0.13832 > -1.0289564* > *#@# 4 534 3.31196 15.62417 68.48689 6.17881 0.21339 -0.13215 > -1.0289565* > *#@# 4 561 3.31196 15.62417 68.48689 6.17881 0.14601 -0.13674 > -1.0289570* > *#@# 4 565 3.31196 15.62417 68.48689 6.17881 0.13447 -0.13674 > -1.0289571* > *Powell done niters total = 4* > *OptTimeSec 24.2 sec* > *OptTimeMin 0.40 min* > *nEvals 580* > *Final parameters 3.31203771 15.61334038 68.42005920 6.18280220 > 0.13176514 -0.13576585 * > *Final cost -1.028957125573420* > > > *---------------------------------* > *sep = 2 -----------------------------------* > > > *---------------------------------* > *Init Powel Params dof = 6* > *Starting OpenPowel2(), sep = 2* > *InitialCost -1.0287065506 * > *#@# 2 582 3.31204 15.61334 68.42006 6.18280 0.13177 -0.13577 > -1.0287066* > *fs_powell::minimize* > * nparams 6* > * maxfev 4* > * ftol 0.000000* > * linmin_xtol_ 0.001000* > * powell nthiter 0: fret = -1.028707* > *#@# 2 589 3.10392 15.61334 68.42006 6.18280 0.13177 -0.13577 > -1.0287081* > *#@# 2 604 3.09369 14.99531 68.42006 6.18280 0.13177 -0.13577 > -1.0287125* > *#@# 2 606 3.09369 15.04368 68.42006 6.18280 0.13177 -0.13577 > -1.0287126* > *#@# 2 621 3.09369 15.04550 68.23710 6.18280 0.13177 -0.13577 > -1.0287137* > *#@# 2 622 3.09369 15.04550 68.21909 6.18280 0.13177 -0.13577 > -1.0287138* > *#@# 2 630 3.09369 15.04550 68.21119 7.18280 0.13177 -0.13577 > -1.0287204* > *#@# 2 635 3.09369 15.04550 68.21119 7.02697 0.13177 -0.13577 > -1.0287205* > *#@# 2 636 3.09369 15.04550 68.21119 7.06769 0.13177 -0.13577 > -1.0287206* > *#@# 2 650 3.09369 15.04550 68.21119 7.08699 0.03346 -0.13577 > -1.0287210* > *#@# 2 657 3.09369 15.04550 68.21119 7.08699 0.02114 0.86423 > -1.0287254* > * powell nthiter 1: fret = -1.028725* > *#@# 2 681 3.12473 15.04550 68.21119 7.08699 0.02114 0.95289 > -1.0287255* > *#@# 2 695 3.12664 15.42746 68.21119 7.08699 0.02114 0.95289 > -1.0287271* > *#@# 2 696 3.12664 15.34841 68.21119 7.08699 0.02114 0.95289 > -1.0287273* > *#@# 2 720 3.12664 15.32519 68.20757 7.08297 0.02114 0.95289 > -1.0287274* > *#@# 2 724 3.12664 15.32519 68.20757 7.07547 0.02114 0.95289 > -1.0287275* > *#@# 2 745 3.12664 15.32519 68.20757 7.07447 0.01759 0.81959 > -1.0287278* > *#@# 2 762 3.14700 15.49804 68.20535 7.06672 0.01540 0.72493 > -1.0287280* > * powell nthiter 2: fret = -1.028728* > *#@# 2 792 3.14765 15.49494 68.20538 7.06686 0.01544 0.59641 > -1.0287281* > *#@# 2 803 3.14765 15.49494 68.11650 7.06686 0.01544 0.59810 > -1.0287282* > *#@# 2 804 3.14765 15.49494 68.14099 7.06686 0.01544 0.59810 > -1.0287284* > *#@# 2 805 3.14765 15.49494 68.15399 7.06686 0.01544 0.59810 > -1.0287285* > *#@# 2 807 3.14765 15.49494 68.16380 7.06686 0.01544 0.59810 > -1.0287286* > * powell nthiter 3: fret = -1.028729* > *#@# 2 867 3.12259 15.49539 68.16066 7.07157 0.01111 0.59788 > -1.0287287* > *Powell done niters total = 4* > *OptTimeSec 161.2 sec* > *OptTimeMin 2.69 min* > *nEvals 938* > *Final parameters 3.12265301 15.49595165 68.16065216 7.06536150 > 0.01209922 0.59759676 * > *Final cost -1.028728664232616* > > > *---------------------------------* > *mri_coreg utimesec 241.181825* > *mri_coreg stimesec 0.360032* > *mri_coreg ru_maxrss 504732* > *mri_coreg ru_ixrss 0* > *mri_coreg ru_idrss 0* > *mri_coreg ru_isrss 0* > *mri_coreg ru_minflt 381121* > *mri_coreg ru_majflt 0* > *mri_coreg ru_nswap 0* > *mri_coreg ru_inblock 71512* > *mri_coreg ru_oublock 16* > *mri_coreg ru_msgsnd 0* > *mri_coreg ru_msgrcv 0* > *mri_coreg ru_nsignals 0* > *mri_coreg ru_nvcsw 505* > *mri_coreg ru_nivcsw 28383* > *Final RefRAS-to-MovRAS* > * 0.99995 0.01043 0.00021 3.12265;* > *-0.01038 0.99235 0.12300 15.49595;* > * 0.00107 -0.12300 0.99241 68.16065;* > * 0.00000 0.00000 0.00000 1.00000;* > *Final RefVox-to-MovVox* > * 0.99995 0.00021 -0.01043 19.00880;* > *-0.01038 0.12300 -0.99235 243.54027;* > *-0.00107 -0.99241 -0.12300 188.07765;* > * 0.00000 0.00000 0.00000 1.00000;* > *Final parameters 3.1227 15.4960 68.1607 7.0654 0.0121 0.5976 * > *nhits = 1287172 out of 16777216, Percent Overlap: 61.4* > *mri_coreg RunTimeSec 241.7 sec* > *To check run:* > * tkregisterfv --mov BS7_PET.lps.nii.gz --targ > /NAS/tupac/matthieu/FS5.3//207118_M0_2014-01-29/mri/brainmask.mgz --reg > Pet2T1.BS7.register.dof6.mri_coreg.lta --s 207118_M0_2014-01-29 --surfs * > > *mri_coreg done* > > > Best regards, > Matthieu > > 2016-09-30 21:07 GMT+02:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> Can you send the mri_coreg terminal output? >> >> >> On 09/29/2016 11:19 AM, Matthieu Vanhoutte wrote: >> > Dear Freesurfer's experts, >> > >> > I would like to register PET image onto T1 anatomical. I used >> > bbregister with the following command and it failed : >> > /bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg >> > Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out >> > Pet2T1.init.register.dof6.dat --o rPET.nii.gz / >> > / >> > / >> > Having heard about mri_coreg solving some bbregister fails, I tested >> > it with the following command : >> > /mri_coreg --s SUBJID --mov PET.nii.gz --reg >> > Pet2T1.register.dof6.mri_coreg.lta --regdat >> > Pet2T1.register.dof6.mri_coreg.dat/ >> > / >> > / >> > But it failed in the same way than bbregister. Do you have any advice >> > on this problem ? >> > >> > Best regards, >> > Matthieu >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
