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/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+Greve%22> > > Sun, 11 Sep 2016 19:14:45 -0700 > <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20160911> > > What is your command line and log file? Sounds like the initial > registration failed. > > > ---------- Forwarded message ---------- > From: *A Nunes* <adonay.s.nu...@gmail.com > <mailto:adonay.s.nu...@gmail.com>> > Date: Sun, Sep 11, 2016 at 7:04 PM > Subject: Tkregister2 error, moveable not present just white screen > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > > 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 > 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 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.
