Hi,<div><br></div><div>Bump?</div><div><br></div><div>Can someone please explain to me the puzzle described below regarding tkregister2 and vox2ras0 (which I thought should be ignored for registration purposes?) </div><div>

<br></div><div>Thanks!</div><div><br></div><div>-- Shay</div><div><br><br><div class="gmail_quote">On Sat, May 26, 2012 at 2:23 PM, Shay Ohayon <span dir="ltr">&lt;<a href="mailto:shay.ohayon@gmail.com" target="_blank">shay.ohayon@gmail.com</a>&gt;</span> wrote:<br>

<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<div><br></div><div>Here&#39;s a question to Doug / anyone else who mastered the intricate way of volume transformations:<br>

<div><br></div><div>I&#39;m a bit puzzled. </div><div>According to Free surfer&#39;s documentation (fscoordinates.pdf), the way two volumes are registered to each other using tkregister is always using</div>
<div>the fixed transformation (tkvox2ras) (see page 6). </div><div><br></div><div>However, when I do the following little experiment (using matlab&#39;s freesurfer API)</div><div><div><br></div><div>A = &#39;001.nii&#39;;</div>


<div>B = &#39;002.nii&#39;;</div><div>X=MRIread(A);</div><div>X.vox2ras0(1,4) = 40;</div><div>MRIwrite(X,B);</div></div><div><br></div><div>tkregister2 --targ 001.nii --mov 002.nii --regheader -reg R.reg</div><div><br></div>


<div>The two volumes are not in alignment when they are loaded into tkregister.</div><div>Now, what am I missing here? </div><div>If both were loaded using the fixed transform, they should still be in alignment (i.e., vox2ras should be ignored for registration purposes).</div>


<div><br></div><div>Thanks in advance,</div><div><br></div><div>-- Shay</div><div>Tsao lab</div><div>Caltech</div><div><br></div><div><br></div><div><br></div><div><br></div></div>
</blockquote></div><br></div>