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]&q=from:%22Douglas+Greve%22>
Sun, 11 Sep 2016 19:14:45 -0700
<http://www.mail-archive.com/[email protected]&q=date:20160911>
What is your command line and log file? Sounds like the initial registration
failed.
---------- Forwarded message ----------
From: A Nunes <[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]>
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
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.
