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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Dr Mori,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thank you very much for your quick and detailed
answers. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<ol style='margin-top:0in' start=1 type=1>
<li class=MsoNormal style='color:navy;mso-list:l2 level1 lfo3'><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial'>One
thing I need to note is that the transformation matrix I have is a “final”
combined matrix of AIR rigid, AIR affine, and LDDMM K map (so it should be
in the raw data format). Can I extract the “vector”
information at the specified location in this transformation matrix? And
how?<o:p></o:p></span></font></li>
</ol>
<p class=MsoNormal style='margin-left:.25in'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<ol style='margin-top:0in' start=2 type=1>
<li class=MsoNormal style='color:navy;mso-list:l2 level1 lfo3'><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial'>I
agree that checking the result after each step is necessary. I have manually
processed and checked all my data. If there is a way to automate the
process by a command file after I have finalized the methods and steps, it
will be nice so that it can help avoid any unintended mistake (forget to
change a parameter, typo, misclick a button etc) which might happen when I
manually process a lot images. So it will be a nice feature, but of course
not a must yet.<o:p></o:p></span></font></li>
</ol>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Yi<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> mristudio-users-bounces@mristudio.org
[mailto:mristudio-users-bounces@mristudio.org] <b><span style='font-weight:
bold'>On Behalf Of </span></b>susumu mori<br>
<b><span style='font-weight:bold'>Sent:</span></b> Saturday, January 30, 2010
8:30 AM<br>
<b><span style='font-weight:bold'>To:</span></b> Yi Jiang; DTI Studio, ROI
Editor, Landmarker Questions/Support; Xin Li; Jiangyang Zhang<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Mristudio-users]
apply transformation to landmarkers & commandfile</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Hi Yi,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Fri, Jan 29, 2010 at 5:25 PM, Yi Jiang <<a
href="mailto:yj3@duke.edu">yj3@duke.edu</a>> wrote:<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Hello, dear all,</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>I have two questions and am wondering if someone can help.</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<ol style='margin-top:0in' start=1 type=1>
<li class=MsoNormal style='mso-list:l0 level1 lfo1'><font size=3 face=Arial><span
style='font-size:12.0pt;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></font><o:p></o:p></li>
</ol>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><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.<o:p></o:p></span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;
margin-left:4.8pt;margin-right:0in'>
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<div>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<ol style='margin-top:0in' start=2 type=1>
<li class=MsoNormal style='mso-list:l1 level1 lfo2'><font size=3 face=Arial><span
style='font-size:12.0pt;font-family: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?</span></font><o:p></o:p></li>
</ol>
</div>
</div>
</blockquote>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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>
<o:p></o:p></span></font></p>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;
margin-left:4.8pt;margin-right:0in'>
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<div>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Thank you very much!</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Have a nice weekend!</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Best</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'>Yi</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face=Arial><span style='font-size:12.0pt;
font-family:Arial'> </span></font><o:p></o:p></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
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<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
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