Hi,<br> Orientation problem is outlined below.<br> 1-When the target in coronal view, movable(example_func) is sagital.<br> 2- When the target is in sagital view, movable is&nbsp; coronal.<br> 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.<br> <br> <br> 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?<br> <br> &nbsp;<br> <br> Regards<br> <br> Uzay<br> <br><br><b><i>Doug Greve &lt;greve@nmr.mgh.harvard.edu&gt;</i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">      <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"><title></title>     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?<br> <br> uzay
 emir wrote: <blockquote cite="mid446892.4810.qm@web55113.mail.re4.yahoo.com" type="cite">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.&nbsp; I think this is something related following lines where I found it in the reg- feat2anat log file. <br> Regards<br>   <br> Uzay<br>   <meta http-equiv="Content-Type" content="text/html; ">   <meta name="Generator" content="Kate, the KDE Advanced Text Editor">   <pre>----------------------------------------------------------------- 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-&gt;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 <br> ----------------------------------------------------------------- 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-&gt;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-&gt;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</pre>   <br>  
 <div> __________________________________________________<br> Do You Yahoo!?<br> Tired of spam? Yahoo! Mail has the best spam protection around <br> <a class="moz-txt-link-freetext" href="http://mail.yahoo.com">http://mail.yahoo.com</a> </div>   <pre wrap=""><hr size="4" width="90%"><br>Fri May 18 11:13:12 EEST 2007<br>/home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig<br>/home/uzay/freesurfer_3/freesurfer/bin//reg-feat2anat<br>--feat Akkaya_Zuhre_1_9++.feat/ --subject akkaya<br>Linux localhost.localdomain 2.6.12-1.1381_FC3 #1 Fri Oct 21 03:46:55 EDT 2005 i686 i686 i386 GNU/Linux<br>mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz<br>mri_convert /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz <br>$Id: mri_convert.c,v 1.141 2007/04/26 05:31:21 greve Exp $<br>reading from
 /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz...<br>TR=11.00, TE=4.92, TI=4.92, flip angle=15.00<br>i_ras = (-1, 2.56273e-11, 6.83856e-10)<br>j_ras = (-1.17877e-09, -2.94451e-16, -1)<br>k_ras = (3.0538e-12, 1, -9.84868e-13)<br>writing to Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/anat.nii.gz...<br>example_func ras_good_flag <br>-------------------------------------------------------<br>Initializing exf2anat from crude std2anat<br>tkregister2 --targ /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz --mov /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img --reg Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat --fslregout Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2anat.fsl.mat --regheader --noedit<br>target  volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz<br>movable volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>reg file      
 Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat<br>LoadVol        0<br>$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $<br>Diagnostic Level -1<br>INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz<br>Ttarg: --------------------<br>-1.000   0.000   0.000   128.000;<br> 0.000   0.000   1.000  -128.000;<br> 0.000  -1.000   0.000   128.000;<br> 0.000   0.000   0.000   1.000;<br>INFO: loading movable /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>Tmov: --------------------<br>-2.000   0.000   0.000   91.000;<br> 0.000   0.000   2.000  -91.000;<br> 0.000  -2.000   0.000   109.000;<br> 0.000   0.000   0.000   1.000;<br>mkheaderreg = 1, float2int = 0<br>Computing reg from header (and possibly input matrix)<br>---- Input registration matrix (computed) --------<br> 1.000   0.000   0.000   1.414;<br>-0.000  -0.000   1.000  -30.612;<br> 0.000  -1.000  -0.000  -44.496;<br> 0.000   0.000   0.000  
 1.000;<br>---------------------------------------<br>---- Input registration matrix --------<br> 1.000   0.000   0.000   1.414;<br>-0.000  -0.000   1.000  -30.612;<br> 0.000  -1.000  -0.000  -44.496;<br> 0.000   0.000   0.000   1.000;<br>subject = subject-unknown<br>RegMat ---------------------------<br> 1.000   0.000   0.000   1.414;<br>-0.000  -0.000   1.000  -30.612;<br> 0.000  -1.000  -0.000  -44.496;<br> 0.000   0.000   0.000   1.000;<br>register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written<br>FSLOUTPUTTYPE NIFTI_GZ <br>tkreg2FSL: mov det = -8, ref det = -1<br>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<br>betfunc Akkaya_Zuhre_1_9++.feat//example_func Akkaya_Zuhre_1_9++.feat//reg/freesurfer/tmp/exfbet<br>Fri May 18 11:13:24 EEST 2007<br>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<br>WARNING: Both reference and input images have an sform matrix set<br>  The output image will use the sform from the reference image<br>-------------------------------------------------------<br>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<br>---- FSL registration matrix --------<br> 0.009  -0.924  -0.383   227.568;<br>-0.306   0.362  -0.880   150.574;<br> 0.952   0.125  -0.279   20.398;<br> 0.000  
 0.000   0.000   1.000;<br>INFO: using NIfTI-1 sform <br>---------------------------------------<br>INFO: no target volume specified, assuming FreeSurfer orig volume.<br>target  volume orig<br>movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz<br>reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat<br>LoadVol        0<br>$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $<br>Diagnostic Level -1<br>INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/orig.mgz<br>Ttarg: --------------------<br>-1.000   0.000   0.000   128.000;<br> 0.000   0.000   1.000  -128.000;<br> 0.000  -1.000   0.000   128.000;<br> 0.000   0.000   0.000   1.000;<br>INFO: using NIfTI-1 sform <br>INFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz<br>Tmov: --------------------<br>-3.000   0.000   0.000   96.000;<br> 0.000   0.000   3.750  -67.500;<br> 0.000  -3.000   0.000   96.000;<br> 0.000   0.000   0.000  
 1.000;<br>mkheaderreg = 0, float2int = 0<br>FSLOUTPUTTYPE NIFTI_GZ <br>fsl2TkReg: mov det = -33.75, ref det = -1<br>---- Input registration matrix (computed) --------<br> 0.009  -0.952  -0.306  -12.434;<br> 0.383  -0.279   0.880  -39.490;<br>-0.924  -0.125   0.362  -1.258;<br> 0.000   0.000   0.000   1.000;<br>---------------------------------------<br>---- Input registration matrix --------<br> 0.009  -0.952  -0.306  -12.434;<br> 0.383  -0.279   0.880  -39.490;<br>-0.924  -0.125   0.362  -1.258;<br> 0.000   0.000   0.000   1.000;<br>subject = akkaya<br>RegMat ---------------------------<br> 0.009  -0.952  -0.306  -12.434;<br> 0.383  -0.279   0.880  -39.490;<br>-0.924  -0.125   0.362  -1.258;<br> 0.000   0.000   0.000   1.000;<br>register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2exf.register.dat written<br>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<br>---- FSL registration matrix --------<br> 1.023  -0.007   0.032  -12.177;<br>-0.001   1.201   0.148  -1.616;<br>-0.014  -0.173   1.167   18.642;<br> 0.000   0.000   0.000   1.000;<br>-----------------------------------------------------------------<br>INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.<br>INFO: use Analyze 7.5 hdr-&gt;hist.orient value: 0, transverse unflipped (default).<br>INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file<br>-----------------------------------------------------------------<br>INFO: using NIfTI-1 sform <br>-----------------------------------------------------------------<br>INFO: could not find
 /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.<br>INFO: use Analyze 7.5 hdr-&gt;hist.orient value: 0, transverse unflipped (default).<br>INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file<br>-----------------------------------------------------------------<br>-----------------------------------------------------------------<br>INFO: could not find /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file for direction cosine info.<br>INFO: use Analyze 7.5 hdr-&gt;hist.orient value: 0, transverse unflipped (default).<br>INFO: if not valid, please provide the information in /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.mat file<br>-----------------------------------------------------------------<br>---------------------------------------<br>target  volume
 /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>movable volume Akkaya_Zuhre_1_9++.feat//example_func.nii.gz<br>reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat<br>LoadVol        0<br>$Id: tkregister2.c,v 1.80 2007/05/11 18:39:00 greve Exp $<br>Diagnostic Level -1<br>INFO: loading target /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>INFO: target does not conform to COR format, so I'm going to<br>reslice to COR. This will not affect the final registration.<br>Ttarg: --------------------<br>-1.000   0.000   0.000   128.000;<br> 0.000   0.000   1.000  -128.000;<br> 0.000  -1.000   0.000   128.000;<br> 0.000   0.000   0.000   1.000;<br>INFO: using NIfTI-1 sform <br>INFO: loading movable Akkaya_Zuhre_1_9++.feat//example_func.nii.gz<br>Tmov: --------------------<br>-3.000   0.000   0.000   96.000;<br> 0.000   0.000   3.750  -67.500;<br> 0.000  -3.000   0.000   96.000;<br> 0.000   0.000   0.000  
 1.000;<br>mkheaderreg = 0, float2int = 0<br>FSLOUTPUTTYPE NIFTI_GZ <br>fsl2TkReg: mov det = -33.75, ref det = -8<br>---- Input registration matrix (computed) --------<br> 0.977  -0.002   0.027  -3.080;<br>-0.012   0.121   0.841   7.974;<br>-0.000  -0.817   0.104   13.120;<br> 0.000   0.000   0.000   1.000;<br>---------------------------------------<br>---- Input registration matrix --------<br> 0.977  -0.002   0.027  -3.080;<br>-0.012   0.121   0.841   7.974;<br>-0.000  -0.817   0.104   13.120;<br> 0.000   0.000   0.000   1.000;<br>subject = subject-unknown<br>RegMat ---------------------------<br> 0.977   0.027   0.002  -3.080;<br>-0.012   0.841  -0.121   7.974;<br>-0.000   0.104   0.817   13.120;<br> 0.000   0.000   0.000   1.000;<br>register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/std2exf.register.dat written<br>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<br>-------------------------------------------------------<br>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<br>---- FSL registration matrix --------<br> 0.005  -0.801  -0.227   230.557;<br>-0.309   0.189  -0.770   161.466;<br> 0.927   0.070  -0.273   36.893;<br> 0.000   0.000   0.000   1.000;<br>---------------------------------------<br>target  volume /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz<br>movable volume /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>reg file       Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat<br>LoadVol        0<br>$Id: tkregister2.c,v 1.80 2007/05/11
 18:39:00 greve Exp $<br>Diagnostic Level -1<br>INFO: loading target /home/uzay/freesurfer_3/freesurfer/subjects/akkaya/mri/brainmask.mgz<br>Ttarg: --------------------<br>-1.000   0.000   0.000   128.000;<br> 0.000   0.000   1.000  -128.000;<br> 0.000  -1.000   0.000   128.000;<br> 0.000   0.000   0.000   1.000;<br>INFO: loading movable /home/uzay/freesurfer_3/freesurfer/fsl/etc/standard/avg152T1_brain.img<br>Tmov: --------------------<br>-2.000   0.000   0.000   91.000;<br> 0.000   0.000   2.000  -91.000;<br> 0.000  -2.000   0.000   109.000;<br> 0.000   0.000   0.000   1.000;<br>mkheaderreg = 0, float2int = 0<br>FSLOUTPUTTYPE NIFTI_GZ <br>fsl2TkReg: mov det = -8, ref det = -1<br>---- Input registration matrix (computed) --------<br> 0.004  -0.964  -0.343  -7.962;<br> 0.287  -0.361   1.086  -58.034;<br>-1.166  -0.108   0.305  -10.228;<br> 0.000   0.000   0.000   1.000;<br>---------------------------------------<br>---- Input registration matrix --------<br> 0.004  -0.964 
 -0.343  -7.962;<br> 0.287  -0.361   1.086  -58.034;<br>-1.166  -0.108   0.305  -10.228;<br> 0.000   0.000   0.000   1.000;<br>subject = akkaya<br>RegMat ---------------------------<br> 0.004  -0.964  -0.343  -7.962;<br> 0.287  -0.361   1.086  -58.034;<br>-1.166  -0.108   0.305  -10.228;<br> 0.000   0.000   0.000   1.000;<br>register: file Akkaya_Zuhre_1_9++.feat//reg/freesurfer/anat2std.register.dat written<br>To visually check your results, run:<br>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<br>Fri May 18 11:14:51 EEST 2007<br>reg-feat2anat done<br>  </pre> </blockquote> <br> <pre class="moz-signature" cols="72">-- <br>Douglas N. Greve, Ph.D.<br>MGH-NMR Center<br><a class="moz-txt-link-abbreviated" href="mailto:greve@nmr.mgh.harvard.edu">greve@nmr.mgh.harvard.edu</a><br>Phone Number:
 617-724-2358 <br>Fax: 617-726-7422<br><br>In order to help us help you, please follow the steps in:<br>surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<br><br></pre> </blockquote><br><p>&#32;
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