[Freesurfer] Fwd: Tkregister2 error, moveable not present just white screen

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 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

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