<div>Hi,</div><div> </div><div>I fixed a grammatical error in <font color="#ff0000">red</font> my email. Sorry about my grammatical blunder.</div><div> </div><div>thank you,</div><div>John<br><br></div><div class="gmail_quote">
On Fri, Jul 29, 2011 at 8:42 AM, John Drozd <span dir="ltr"><<a href="mailto:john.drozd@gmail.com">john.drozd@gmail.com</a>></span> wrote:<br><blockquote style="margin: 0px 0px 0px 0.8ex; padding-left: 1ex; border-left-color: rgb(204, 204, 204); border-left-width: 1px; border-left-style: solid;" class="gmail_quote">
<div>Hi,</div><div> </div><div>I and my colleague are using Tom's diffeomorphic demons finite difference algorithm (that I found on the Insight Journal) to warp a nifti MRI ADNI image1 (what I cll my atlas) to another nifti MRI ADNI image2 (what I call my subject). Both images have float pixel types. I am using 5 levels of 15 iterations each with a sigma of 0.8. I notice that when the range between the minimum Jacobian and maximum Jacobian is smaller, the warping is more accurate.</div>
<div> </div><div>I first affine register the atlas to the subject and get a .tfm transform file.</div><div> </div><div>I input this .tfm transform file into the diffeomorphic demons code and warp the atlas to the subject.</div>
<div>This generates a deformation field which I use to warp the atlas grey scale image to the subject grey scale image. The warped atlas looks identical to the subject.</div><div> </div><div>My atlas has a manually traced hippocampus, and so does my subject. These manual tracings were done by an anatomist.</div>
<div> </div><div>When I warp the atlas's label map of the hippocampus to the subject<font color="#ff0000">, the</font> warped hippocampus label map does not match the traced hippocampus of the subject. One side looks close but the other side is off, as if the the warped hippocampus was twisted. We find that it is more accurate when an interpolator is not used on warping the label map, and when an interpolator is used when warping the grey scale image. Am I and my colleague doing something wrong?</div>
<div> </div><div>Thank you for your time.</div><div> </div><div>John<br clear="all"><br>-- <br></div><div>John Drozd<br></div>
<div>Post-Doctoral Fellow, Robarts Research Institute</div>
<div>The University of Western Ontario</div>
<div>London, ON, Canada</div><div><a href="http://publish.uwo.ca/~jdrozd2/index.htm" target="_blank">http://publish.uwo.ca/~jdrozd2/index.htm</a></div>
<div> </div><br>
</blockquote></div><br><br clear="all"><br>-- <br><div>John Drozd<br></div>
<div>Post-Doctoral Fellow, Robarts Research Institute</div>
<div>The University of Western Ontario</div>
<div>London, ON, Canada</div><div><a href="http://publish.uwo.ca/~jdrozd2/index.htm" target="_blank">http://publish.uwo.ca/~jdrozd2/index.htm</a></div>
<div> </div><br>