Hi Yi,<br><br><div class="gmail_quote">On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang <span dir="ltr"><<a href="mailto:yj3@duke.edu">yj3@duke.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial;">Hello, dear all,</span></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"> </font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial;">I have two questions and am wondering if someone can
help.</span></p>
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<li style="margin: 0in 0in 0pt;" class="MsoNormal"><span style="font-family: Arial;">I have already had a
transformation matrix to map the subject image onto the template image, which
was generated by combining AIR rigid, AIR affine, and LDDMM matrix. I want to
define some landmarkers on the subject image, and apply the transformation
matrix to the landmarkers (to see their corresponding location on the template
image). How can I do that?</span></li></ol></div></div></blockquote><div><br>I think this is exactly what the K and H maps are. I need confirmation from Xin, but in my understanding, these transformation matrices contain vectors at each coordinate, indicating where is the new location. If I'm not mistaken, it is Vector (x, y, z) x X-dimension x Y-dimension x Z-dimension. There must be a way to extarct the "Vector" information at the specified coordinate.<br>
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<li style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial">I would like to use the “load command file”
function. I will do AIR linear rigid transformation, AIR linear affine
transformation, image format change to byte, automatic intensity correction by
histogram, and 2-channel LDDMM. Is it possible to put all these into one
command file? If yes, can anyone give me an example file?</font></li></ol></div></div></blockquote><div>I believe the command file is only for the functions within the same box, including byte-integer-float conversion, axial-sagittal-coronal conversion, resampling, etc. They don't include transformation functions. We are working on automation, which will take several months. Meanwhile, I believe it is good idea to use the current way, which forces you to check the result after each step. Transformation sometimes does silly things. Some images may have quality problems. You may want compare different methods (e.g. Mutual Info linear transformation vs AIR, intensity correction methods, contrast of choice). I think it's very important to get a feel about your data and each transformation step. Also, depending on pathology, the transformation strategy may change. Some disease groups have severe intensity changes (e.g. stroke), some have severely enlarged ventricles. You may find the same methods may work for one but not the other. Automation is still a difficult matter for transformation-based analysis.<br>
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<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"> </font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial">Thank you very
much!</font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"> </font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial">Have a nice
weekend!</font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"> </font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial">Best</font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial">Yi</font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"> </font></p>
<p style="margin: 0in 0in 0pt;" class="MsoNormal"><font face="Arial"></font> </p></div></div>
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