Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg

12 Oct 2016

      Thank you for your diagnosis Douglas. How could I get the voxel sizes right
from input nifti pet and mri data ?
Best regards,
Matthieu
Le 12 oct. 2016 10:05 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu a
écrit :
...
The problem appears to be that the PET or the MRI (or both) have
incorrect voxel sizes (about 15%). You need to fix the problem. You can
get a decent registration using something like
mri_coreg --mov BS7_PET.lps.nii.gz --s 207118_FS_Filedrop --reg
dof9.wb.lta --dof 9 --no-ref-mask --ref mri/orig.mgz
with 9 DOF instead of 6 to account for the scaling (voxel size error).
But it is *much* better to get the voxel sizes right and use 6 dof
On 10/06/2016 02:50 PM, Matthieu Vanhoutte wrote:
...
Hi Douglas,
Dis you have time to take a look at ?
Best regards,
Matthieu
Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte"
<matthieuvanhoutte@gmail.com mailto:matthieuvanhoutte@gmail.com> a
écrit :
Hi Douglas,

I have just sent it to you on Filedrop.

Best regards,
Matthieu

2016-10-03 17:45 GMT+02:00 Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@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
    <greve@nmr.mgh.harvard.edu <mailto:greve@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
        >
        >
        > _______________________________________________
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Freesurfer mailing list
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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Re: [Freesurfer] PET/MRI registration failed with bbregister or mri_coreg