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
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>> 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.
>>
>>
>
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> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
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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.

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