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 <greve@nmr.mgh.harvard.edu> 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/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.nunes@gmail.com
> <mailto:adonay.s.nunes@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
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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