It sounds like something has to be fixed. Is the example_func to standard space registration correct? If not, then you will need to fix it. 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 in this situation is that there is an angle between movable and target.


I followed all the steps. Right now should I expect that reg-feat2anat solves the big problems or should i have to register manually with tkregister2?

 

Regards

Uzay


Doug Greve <greve@nmr.mgh.harvard.edu> 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 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 = 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   0.000     1.000;  ---------------------------------------  ---- 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_GZ   tkreg2FSL: 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;   0.000     0.000   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 sform   INFO: 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   0.000     1.000;  mkheaderreg = 0, float2int = 0  FSLOUTPUTTYPE NIFTI_GZ   fsl2TkReg: 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 sform   INFO: 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   0.000     1.000;  mkheaderreg = 0, float2int = 0  FSLOUTPUTTYPE NIFTI_GZ   fsl2TkReg: 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_GZ   fsl2TkReg: 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  greve@nmr.mgh.harvard.edu  Phone Number:   617-724-2358   Fax: 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  greve@nmr.mgh.harvard.edu  Phone Number: 617-724-2358   Fax: 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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