Le 3 oct. 2016 6:25 PM, "Matthieu Vanhoutte" <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>:
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>:

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
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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
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