Hi Dough, Thanks for your help. I was using the preprocessed thinking that after motion correction it would be more accurate and --init-header because they where acquired in the same session. I changed to a raw moveable and the results did not change for the following:
With -init-fsl the moveable is now showing, but about 40% of the subjects the registration has fail, in many cases the moveable is rotated with respect to the target. I tried to use -init-spm but then the moveable and target don't even overlay. I also tried to use a successful registration .dat from another subject using the command --init-reg $SUBJECTS_DIR/subj2/mri/register.dat but the registration is not accurate. In many cases there is the WARNING: initial G-W contrast was negative, but expected positive. If the mov data has a T1 contrast, re-run with --T1. if I run the same command changing --bold to --T1 the results aren't good, as well as if I try -int $SUBJECTS_DIR/subj//T1.mgz. Is there anything else to try rather than manual registration? I just have the T1 and the fmri. Would you recommend another registration method? Thanks Adonay On Mon, Sep 12, 2016 at 12:37 PM, Douglas N Greve <[email protected] > wrote: > I think the problem is the initialization. I noticed you used > --init-header. This should only be used if the two volumes were acquired > during the same session and the direction cosines (ie, geometry) info is > accurate for both. Is this the case? I noticed that the input has > "preproc" in the name, so I'm a bit suspicious. You can try --init-fsl > instead > > > On 09/12/2016 01:36 PM, A Nunes wrote: > > Hi Doug > > > > I can't see any errors in the log file, and with other datasets I did > > not have this issue. My register.dat is: > > > > 50664 > > 3.000000 > > 4.500000 > > 0.150000 > > 9.996076822280884e-01 -2.117119915783405e-02 -1.833262108266354e-02 > > 3.139470825195312e+02 > > 1.872027479112148e-02 1.825972087681293e-02 9.996579289436340e-01 > > 2.150849456787109e+02 > > -2.082921005785465e-02 -9.996089935302734e-01 1.864889077842236e-02 > > 4.339286499023438e+02 > > 0 0 0 1 > > round > > > > and my register.dat.log is: > > > > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 > > cd /Users/adonay/Desktop/data/prepo_cpac > > /Applications/freesurfer/bin/bbregister --s 50664 --mov > > 50664_preprocessed.nii.gz --init-header --reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --bold > > > > $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ > > Darwin sc-155014 15.6.0 Darwin Kernel Version 15.6.0: Mon Aug 29 > > 20:21:34 PDT 2016; root:xnu-3248.60.11~1/RELEASE_X86_64 x86_64 > > FREESURFER_HOME /Applications/freesurfer > > mri_convert 50664_preprocessed.nii.gz > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > mri_convert 50664_preprocessed.nii.gz > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from 50664_preprocessed.nii.gz... > > TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, -0, 0) > > j_ras = (-0, 1, 0) > > k_ras = (-0, -0, 1) > > writing to > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii... > > tkregister2_cmdl --s 50664 --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --regheader --reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > --noedit > > tkregister_tcl /Applications/freesurfer/tktools/tkregister2.tcl > > INFO: no target volume specified, assuming FreeSurfer orig volume. > > target volume orig > > movable volume > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > reg file > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > LoadVol 0 > > ZeroCRAS 0 > > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > > Diagnostic Level -1 > > INFO: loading target > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/orig.mgz > > Ttarg: -------------------- > > -1.000 0.000 0.000 128.000; > > 0.000 0.000 1.000 -128.000; > > 0.000 -1.000 0.000 128.000; > > 0.000 0.000 0.000 1.000; > > INFO: loading movable > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > Tmov: -------------------- > > -3.000 0.000 0.000 96.000; > > 0.000 0.000 4.500 -63.000; > > 0.000 -3.000 0.000 96.000; > > 0.000 0.000 0.000 1.000; > > mkheaderreg = 1, float2int = 0 > > Computing reg from header (and possibly input matrix) > > ---- Input registration matrix (computed) -------- > > 1.000 0.000 0.000 307.685; > > 0.000 0.000 1.000 216.216; > > 0.000 -1.000 0.000 435.341; > > 0.000 0.000 0.000 1.000; > > --------------------------------------- > > ---- Input registration matrix -------- > > 1.000 0.000 0.000 307.685; > > 0.000 0.000 1.000 216.216; > > 0.000 -1.000 0.000 435.341; > > 0.000 0.000 0.000 1.000; > > Determinant 1 > > subject = 50664 > > RegMat --------------------------- > > 1.000 0.000 0.000 307.685; > > 0.000 0.000 1.000 216.216; > > 0.000 -1.000 0.000 435.341; > > 0.000 0.000 0.000 1.000; > > mri_segreg --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --init-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > --out-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 > > 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 > > $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ > > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 > > cd /Users/adonay/Desktop/data/prepo_cpac > > mri_segreg --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --init-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > --out-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 > > 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 > > sysname Darwin > > hostname sc-155014 > > machine x86_64 > > user adonay > > movvol > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > regfile > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.init.dat > > subject 50664 > > dof 6 > > outregfile > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > UseMask 0 > > UseLH 1 > > UseRH 1 > > nsubsamp 100 > > PenaltySign -1 > > PenaltySlope 0.500000 > > PenaltyCenter 0.000000 > > surfname white > > GMProjFrac 0.500000 > > WMProjAbs 2.000000 > > lhcostfile (null) > > rhcostfile (null) > > interp trilinear (1) > > frame 0 > > TolPowell 0.000100 > > nMaxItersPowell 36 > > n1dmin 3 > > Profile 0 > > Gdiag_no -1 > > AddNoise 0 (0) > > SynthSeed 1473407392 > > TransRandMax 0.000000 > > RotRandMax 0.000000 > > Translations 0.000000 0.000000 0.000000 > > Rotations 0.000000 0.000000 0.000000 > > Input reg > > 1.000 0.000 0.000 307.685; > > 0.000 0.000 1.000 216.216; > > 0.000 -1.000 0.000 435.341; > > 0.000 0.000 0.000 1.000; > > > > Loading mov > > Extracting frame 0 > > Projecting LH Surfs > > Loading lh.white surf > > Loading lh.thickness for GM > > GM Proj: 1 0.500000 2.000000 > > WM Proj: 0 0.500000 2.000000 > > Projecting RH Surfs > > Loading rh.white surf > > Loading rh.thickness > > Projecting RH Surfs > > Computing relative cost > > 0 -25.0 -25.0 -25.0 10.000000 > > 1 -25.0 -25.0 25.0 10.000000 > > 2 -25.0 25.0 -25.0 10.000000 > > 3 -25.0 25.0 25.0 10.000000 > > 4 25.0 -25.0 -25.0 10.000000 > > 5 25.0 -25.0 25.0 10.000000 > > 6 25.0 25.0 -25.0 10.000000 > > 7 25.0 25.0 25.0 10.000000 > > REL: 8 10.000000 80.000000 10.000000 rel = 1 > > Initial costs ---------------- > > Number of surface hits 0 > > WM Intensity nan +/- nan > > Ctx Intensity nan +/- nan > > Pct Contrast nan +/- nan > > Cost 10.0000 > > RelCost 1.0000 > > > > ------------------------------------ > > Brute force preopt -4 4 4, n = 729 > > 0 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 -4.0000 > > 10.0000 10.0000 0.0 > > Brute Force -------------------------- > > Min cost was 10.000000 > > Number of iterations 729 > > Search time 0.723000 sec > > Parameters at best (transmm, rotdeg) > > -4.000 -4.000 -4.000 -4.000 -4.000 -4.000 > > -------------------------------------------- > > > > Starting Powell Minimization > > Init Powel Params dof = 6 > > 0 -4 > > 1 -4 > > 2 -4 > > 3 -4 > > 4 -4 > > 5 -4 > > Powell done niters = 0 > > Computing relative cost > > 0 -25.0 -25.0 -25.0 10.000000 > > 1 -25.0 -25.0 25.0 10.000000 > > 2 -25.0 25.0 -25.0 10.000000 > > 3 -25.0 25.0 25.0 10.000000 > > 4 25.0 -25.0 -25.0 10.000000 > > 5 25.0 -25.0 25.0 10.000000 > > 6 25.0 25.0 -25.0 10.000000 > > 7 25.0 25.0 25.0 10.000000 > > REL: 8 10.000000 80.000000 10.000000 rel = 1 > > Number of iterations 0 > > Min cost was 10.000000 > > Number of FunctionCalls 109 > > TolPowell 0.000100 > > nMaxItersPowell 36 > > OptimizationTime 0.105000 sec > > Parameters at optimum (transmm) -1.38389 -1.38389 -1.38389 > > Parameters at optimum (rotdeg) -1.38389 -1.38389 -1.38389 > > Final costs ---------------- > > Number of surface hits 0 > > WM Intensity nan +/- nan > > Ctx Intensity nan +/- nan > > Pct Contrast nan +/- nan > > Cost 10.0000 > > RelCost 1.0000 > > Reg at min cost was > > 0.999 0.024 0.025 301.214; > > -0.024 -0.025 0.999 218.039; > > 0.024 -0.999 -0.024 435.913; > > 0.000 0.000 0.000 1.000; > > > > Writing optimal reg to > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat, > > type = 14 > > Original Reg > > 1.000 0.000 0.000 307.685; > > 0.000 0.000 1.000 216.216; > > 0.000 -1.000 0.000 435.341; > > 0.000 0.000 0.000 1.000; > > > > Original Reg - Optimal Reg > > 0.001 -0.024 -0.025 6.471; > > 0.024 0.025 0.001 -1.823; > > -0.024 -0.001 0.024 -0.573; > > 0.000 0.000 0.000 0.000; > > > > Computing change in lh position > > LH rmsDiffMean 6.969701 > > Computing change in rh position > > Surface RMS Diff (mm) 6.712317 9.940387 > > mri_segreg done > > mri_segreg --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --init-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > --out-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --brute > > -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d > > 1e-3 --c0 0 --mincost > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.mincost > > --dof 6 --nmax 36 --param > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.param > > --surf white --cur-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.curopt.dat > > --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 > > $Id: mri_segreg.c,v 1.103.2.1 2011/10/07 19:14:42 greve Exp $ > > setenv SUBJECTS_DIR /Users/adonay/Desktop/data/freesurfer/5 > > cd /Users/adonay/Desktop/data/prepo_cpac > > mri_segreg --mov > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > --init-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > --out-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --brute > > -0.1 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d > > 1e-3 --c0 0 --mincost > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.mincost > > --dof 6 --nmax 36 --param > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat.param > > --surf white --cur-reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/reg.curopt.dat > > --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 > > sysname Darwin > > hostname sc-155014 > > machine x86_64 > > user adonay > > movvol > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/template.nii > > regfile > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp. > bbregister.14726/bbr.pass1.dat > > subject 50664 > > dof 6 > > outregfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/ > register.dat > > UseMask 0 > > UseLH 1 > > UseRH 1 > > nsubsamp 1 > > PenaltySign -1 > > PenaltySlope 0.500000 > > PenaltyCenter 0.000000 > > surfname white > > GMProjFrac 0.500000 > > WMProjAbs 2.000000 > > lhcostfile (null) > > rhcostfile (null) > > interp trilinear (1) > > frame 0 > > TolPowell 0.000000 > > nMaxItersPowell 36 > > n1dmin 3 > > Profile 0 > > Gdiag_no -1 > > AddNoise 0 (0) > > SynthSeed 1474349903 > > TransRandMax 0.000000 > > RotRandMax 0.000000 > > Translations 0.000000 0.000000 0.000000 > > Rotations 0.000000 0.000000 0.000000 > > Input reg > > 0.999 0.024 0.025 301.214; > > -0.024 -0.025 0.999 218.039; > > 0.024 -0.999 -0.024 435.913; > > 0.000 0.000 0.000 1.000; > > > > Loading mov > > Extracting frame 0 > > Projecting LH Surfs > > Loading lh.white surf > > Loading lh.thickness for GM > > GM Proj: 1 0.500000 2.000000 > > WM Proj: 0 0.500000 2.000000 > > Projecting RH Surfs > > Loading rh.white surf > > Loading rh.thickness > > Projecting RH Surfs > > Computing relative cost > > 0 -25.0 -25.0 -25.0 10.000000 > > 1 -25.0 -25.0 25.0 10.000000 > > 2 -25.0 25.0 -25.0 10.000000 > > 3 -25.0 25.0 25.0 10.000000 > > 4 25.0 -25.0 -25.0 10.000000 > > 5 25.0 -25.0 25.0 10.000000 > > 6 25.0 25.0 -25.0 10.000000 > > 7 25.0 25.0 25.0 10.000000 > > REL: 8 10.000000 80.000000 10.000000 rel = 1 > > Initial costs ---------------- > > Number of surface hits 0 > > WM Intensity nan +/- nan > > Ctx Intensity nan +/- nan > > Pct Contrast nan +/- nan > > Cost 10.0000 > > RelCost 1.0000 > > > > ------------------------------------ > > Brute force preopt -0.1 0.1 0.1, n = 729 > > 0 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 -0.1000 > > 10.0000 10.0000 0.0 > > Brute Force -------------------------- > > Min cost was 10.000000 > > Number of iterations 729 > > Search time 0.976000 sec > > Parameters at best (transmm, rotdeg) > > -0.100 -0.100 -0.100 -0.100 -0.100 -0.100 > > -------------------------------------------- > > > > Starting Powell Minimization > > Init Powel Params dof = 6 > > 0 -0.1 > > 1 -0.1 > > 2 -0.1 > > 3 -0.1 > > 4 -0.1 > > 5 -0.1 > > Powell done niters = 0 > > Computing relative cost > > 0 -25.0 -25.0 -25.0 10.000000 > > 1 -25.0 -25.0 25.0 10.000000 > > 2 -25.0 25.0 -25.0 10.000000 > > 3 -25.0 25.0 25.0 10.000000 > > 4 25.0 -25.0 -25.0 10.000000 > > 5 25.0 -25.0 25.0 10.000000 > > 6 25.0 25.0 -25.0 10.000000 > > 7 25.0 25.0 25.0 10.000000 > > REL: 8 10.000000 80.000000 10.000000 rel = 1 > > Number of iterations 0 > > Min cost was 10.000000 > > Number of FunctionCalls 109 > > TolPowell 0.000000 > > nMaxItersPowell 36 > > OptimizationTime 3.303000 sec > > Parameters at optimum (transmm) 2.51611 2.51611 2.51611 > > Parameters at optimum (rotdeg) 2.51611 2.51611 2.51611 > > Final costs ---------------- > > Number of surface hits 0 > > WM Intensity nan +/- nan > > Ctx Intensity nan +/- nan > > Pct Contrast nan +/- nan > > Cost 10.0000 > > RelCost 1.0000 > > Reg at min cost was > > 1.000 -0.021 -0.018 313.947; > > 0.019 0.018 1.000 215.085; > > -0.021 -1.000 0.019 433.929; > > 0.000 0.000 0.000 1.000; > > > > Writing optimal reg to > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat, type = > 14 > > Original Reg > > 0.999 0.024 0.025 301.214; > > -0.024 -0.025 0.999 218.039; > > 0.024 -0.999 -0.024 435.913; > > 0.000 0.000 0.000 1.000; > > > > Original Reg - Optimal Reg > > -0.000 0.045 0.043 -12.733; > > -0.043 -0.043 -0.000 2.954; > > 0.045 0.000 -0.043 1.985; > > 0.000 0.000 0.000 0.000; > > > > Computing change in lh position > > LH rmsDiffMean 13.402319 > > Computing change in rh position > > Surface RMS Diff (mm) 13.076895 18.900088 > > mri_segreg done > > Cleaning up > > Started at Thu Sep 8 19:09:02 PDT 2016 > > Ended at Thu Sep 8 19:09:28 PDT 2016 > > BBR-Run-Time-Sec 26 > > bbregister Done > > To check results, run: > > tkregister2 --mov 50664_preprocessed.nii.gz --reg > > /Users/adonay/Desktop/data/freesurfer/5/50664/mri/register.dat --surf > > > > > > > > > > > > Thanks, > > Adonay > > > > Douglas Greve > > <http://www.mail-archive.com/[email protected]. > harvard.edu&q=from:%22Douglas+Greve%22> > > Sun, 11 Sep 2016 19:14:45 -0700 > > <http://www.mail-archive.com/[email protected]. > harvard.edu&q=date:20160911> > > > > What is your command line and log file? Sounds like the initial > > registration failed. > > > > > > ---------- Forwarded message ---------- > > From: *A Nunes* <[email protected] > > <mailto:[email protected]>> > > Date: Sun, Sep 11, 2016 at 7:04 PM > > Subject: Tkregister2 error, moveable not present just white screen > > To: Freesurfer support list <[email protected] > > <mailto:[email protected]>> > > > > > > Hi, > > > > After doing a bbregistration I visualized the results with > > tkregister2. The target is alright, however, the moveable is not > > present, it is just a white screen. > > > > What steps could I take to solve this issue? > > > > Thanks > > Adonay > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > 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 [email protected] 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.
