not yet. I'm on vacation until Wed, so it might be a while.
On 10/6/16 2:50 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"
<matthieuvanhou...@gmail.com <mailto:matthieuvanhou...@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
<gr...@nmr.mgh.harvard.edu <mailto: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 <mailto: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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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<https://gate.nmr.mgh.harvard.edu/filedrop2>
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/>
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