Hi Doug and all,
I just resend this email in case it did not reach, any help will be appreciated.
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.bbregi
ster.14726/template.nii
mri_convert 50664_preprocessed.nii.gz /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.14726/template.nii...
tkregister2_cmdl --s 50664 --mov /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.14726/template.nii
--regheader --reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.14726/template.nii
reg file /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.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.bbregi
ster.14726/template.nii
--init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.14726/reg.init.dat
--out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.14726/template.nii
--init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.14726/reg.init.dat
--out-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.14726/template.nii
regfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.14726/reg.init.dat
subject 50664 dof 6 outregfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.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.bbregi
ster.14726/template.nii
--init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.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.bbregi
ster.14726/template.nii
--init-reg /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.bbregi
ster.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.bbregi
ster.14726/template.nii
regfile /Users/adonay/Desktop/data/freesurfer/5/50664/mri/tmp.bbregi
ster.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.har
vard.edu&q=from:%22Douglas+Greve%22>
Sun, 11 Sep 2016 19:14:45 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.har
vard.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
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