Re: [Freesurfer] reg- feat2anat error-problem

Doug Greve Fri, 01 Jun 2007 06:22:32 -0700

It sounds like something has to be fixed. Is the example_func tostandard space registration correct? If not, then you will need to fixit. That registration is purely FSL.


doug


uzay emir wrote:

Hi,
Orientation problem is outlined below.
1-When the target in coronal view, movable(example_func) is sagital.
2- When the target is in sagital view, movable is  coronal.

3- axial view is teh same both movable and target but The problem inthis situation is that there is an angle between movable and target.

I followed all the steps. Right now should I expect that reg-feat2anatsolves the big problems or should i have to register manually withtkregister2?

Regards

Uzay


Doug Greve <[EMAIL PROTECTED]> wrote:

    What do you mean there was an orientation problem? If you use
    analyze files, then it relies on the FSL reg to std space being
    correct. Is it?

    uzay emir wrote:

    Thank you,it is working now. However, I have anorientation
    problem with automatic registration results. This problem has
    been mentioned before but i could not find any reply.  I think
    this is something related following lines where I found it in the
    reg- feat2anat log file.
    Regards

    Uzay

----------------------------------------------------------------- INFO: could not 
find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file 
for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, 
transverse unflipped (default). INFO: if not valid, please provide the information 
in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file

----------------------------------------------------------------- INFO: using NIfTI-1 sform----------------------------------------------------------------- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file ----------------------------------------------------------------- ----------------------------------------------------------------- INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file



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Fri May 18 11:13:12 EEST 2007
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig
/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat
--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya
Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 
i686 i686 i386 GNU/Linux
mri_convert 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz

mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz $Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $

reading from
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...
TR=11.00, TE=4.92, TI=4.92, flip angle=15.00
i_ras = (-1, 2.56273e-11, 6.83856e-10)
j_ras = (-1.17877e-09, -2.94451e-16, -1)
k_ras = (3.0538e-12, 1, -9.84868e-13)
writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...

example_func ras_good_flag-------------------------------------------------------

Initializing exf2anat from crude std2anat
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img

reg fileAkkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat

LoadVol        0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: --------------------
-2.000   0.000   0.000   91.000;
0.000   0.000   2.000  -91.000;
0.000  -2.000   0.000   109.000;
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   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;

0.000 0.000 0.0001.000;

---------------------------------------
---- Input registration matrix --------
1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---------------------------
1.000   0.000   0.000   1.414;
-0.000  -0.000   1.000  -30.612;
0.000  -1.000  -0.000  -44.496;
0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat 
written

FSLOUTPUTTYPE NIFTI_GZtkreg2FSL: mov det = -8, ref det = -1

mri_matrix_multiply -fsl -bin -iim 
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -iim 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat -om 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat
betfunc Akkaya_Zuhre_1_9++.feat//example_func 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet
Fri May 18 11:13:24 EEST 2007
flirt -ref
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz -in 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet.nii.gz -init 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.init.fsl.mat -out 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exf-in-anat -interp trilinear -omat 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat -cost corratio -dof 6 
-searchrx -90 90 -searchry -90 90 -searchrz -90 90
WARNING: Both reference and input images have an sform matrix set
 The output image will use the sform from the reference image
-------------------------------------------------------
tkregister2 --s akkaya --mov Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat --fslreg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat --noedit --mgz
---- FSL registration matrix --------
0.009  -0.924  -0.383   227.568;
-0.306   0.362  -0.880   150.574;
0.952   0.125  -0.279   20.398;

0.0000.000 0.000 1.000;INFO: using NIfTI-1 sform---------------------------------------

INFO: no target volume specified, assuming FreeSurfer orig volume.
target  volume orig
movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/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: using NIfTI-1 sformINFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz

Tmov: --------------------
-3.000   0.000   0.000   96.000;
0.000   0.000   3.750  -67.500;
0.000  -3.000   0.000   96.000;

0.000 0.000 0.0001.000;

mkheaderreg = 0, float2int = 0

FSLOUTPUTTYPE NIFTI_GZfsl2TkReg: mov det = -33.75, ref det = -1

---- Input registration matrix (computed) --------
0.009  -0.952  -0.306  -12.434;
0.383  -0.279   0.880  -39.490;
-0.924  -0.125   0.362  -1.258;
0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
0.009  -0.952  -0.306  -12.434;
0.383  -0.279   0.880  -39.490;
-0.924  -0.125   0.362  -1.258;
0.000   0.000   0.000   1.000;
subject = akkaya
RegMat ---------------------------
0.009  -0.952  -0.306  -12.434;
0.383  -0.279   0.880  -39.490;
-0.924  -0.125   0.362  -1.258;
0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat 
written
tkregister2 --targ 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --mov 
Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --fslreg
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat --noedit
---- FSL registration matrix --------
1.023  -0.007   0.032  -12.177;
-0.001   1.201   0.148  -1.616;
-0.014  -0.173   1.167   18.642;
0.000   0.000   0.000   1.000;
-----------------------------------------------------------------
INFO: could not find 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for 
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------

INFO: using NIfTI-1 sform-----------------------------------------------------------------

INFO: could not find
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for 
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
-----------------------------------------------------------------
INFO: could not find 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for 
direction cosine info.
INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).
INFO: if not valid, please provide the information in 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file
-----------------------------------------------------------------
---------------------------------------
target  volume
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz
reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
INFO: target does not conform to COR format, so I'm going to
reslice to COR. This will not affect the final registration.
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: using NIfTI-1 sformINFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz

Tmov: --------------------
-3.000   0.000   0.000   96.000;
0.000   0.000   3.750  -67.500;
0.000  -3.000   0.000   96.000;

0.000 0.000 0.0001.000;

mkheaderreg = 0, float2int = 0

FSLOUTPUTTYPE NIFTI_GZfsl2TkReg: mov det = -33.75, ref det = -8

---- Input registration matrix (computed) --------
0.977  -0.002   0.027  -3.080;
-0.012   0.121   0.841   7.974;
-0.000  -0.817   0.104   13.120;
0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------
0.977  -0.002   0.027  -3.080;
-0.012   0.121   0.841   7.974;
-0.000  -0.817   0.104   13.120;
0.000   0.000   0.000   1.000;
subject = subject-unknown
RegMat ---------------------------
0.977   0.027   0.002  -3.080;
-0.012   0.841  -0.121   7.974;
-0.000   0.104   0.817   13.120;
0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat 
written
mri_matrix_multiply -fsl -im 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat -iim 
Akkaya_Zuhre_1_9++.feat//reg/example_func2standard.mat -om
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat
-------------------------------------------------------
tkregister2 --s akkaya --targ 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslreg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --noedit
---- FSL registration matrix --------
0.005  -0.801  -0.227   230.557;
-0.309   0.189  -0.770   161.466;
0.927   0.070  -0.273   36.893;
0.000   0.000   0.000   1.000;
---------------------------------------
target  volume 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz
movable volume 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat
LoadVol        0
$Id: tkregister2.c,v 1.80 2007/05/11
18:39:00 greve Exp $
Diagnostic Level -1
INFO: loading target 
/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.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 
/home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img
Tmov: --------------------
-2.000   0.000   0.000   91.000;
0.000   0.000   2.000  -91.000;
0.000  -2.000   0.000   109.000;
0.000   0.000   0.000   1.000;
mkheaderreg = 0, float2int = 0

FSLOUTPUTTYPE NIFTI_GZfsl2TkReg: mov det = -8, ref det = -1

---- Input registration matrix (computed) --------
0.004  -0.964  -0.343  -7.962;
0.287  -0.361   1.086  -58.034;
-1.166  -0.108   0.305  -10.228;
0.000   0.000   0.000   1.000;
---------------------------------------
---- Input registration matrix --------

0.004 -0.964-0.343 -7.962;

0.287  -0.361   1.086  -58.034;
-1.166  -0.108   0.305  -10.228;
0.000   0.000   0.000   1.000;
subject = akkaya
RegMat ---------------------------
0.004  -0.964  -0.343  -7.962;
0.287  -0.361   1.086  -58.034;
-1.166  -0.108   0.305  -10.228;
0.000   0.000   0.000   1.000;
register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat 
written
To visually check your results, run:
tkregister2 --s akkaya --mov Akkaya_Zuhre_1_9++.feat//example_func.nii.gz --reg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat --fslreg 
Akkaya_Zuhre_1_9++.feat//reg/freesurfer/exf2anat.fsl.mat --surf orig --tag
Fri May 18 11:14:51 EEST 2007
reg-feat2anat done


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number:

617-724-2358Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]

Phone Number: 617-724-2358Fax: 617-726-7422


In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] reg- feat2anat error-problem

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