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<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">Hello, Dr
Mori,</SPAN><?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><FONT size=3><FONT
face="Times New Roman"> <o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">Thank you very much for your reply.
It's very clear. Also, I really appreciate all the help from Xin and Anthony.
They are really quick and helpful, and they have solved all my problems so
far.</SPAN><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><FONT size=3><FONT
face="Times New Roman"> <o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">I have one more
question:</SPAN><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><FONT size=3><FONT
face="Times New Roman"> <o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">It seems there is no manual or
instruction about using LDDMM with manually placed landmarkers. Is there such a
function? Or is the current LDDMM only working without landmarker? If yes, how
do we do that? Just add some landmarkers and then start a LDDMM
job?</SPAN><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><FONT size=3><FONT
face="Times New Roman"> <o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">Thank you!</SPAN><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><FONT size=3><FONT
face="Times New Roman"> <o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">Best,</SPAN><o:p></o:p></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt">Yi</SPAN></P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt" class=MsoNormal><SPAN
style="FONT-FAMILY: Arial; FONT-SIZE: 10pt"></SPAN><o:p></o:p> </P></FONT>-----
Original Message ----- </DIV>
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style="BORDER-LEFT: #000000 2px solid; PADDING-LEFT: 5px; PADDING-RIGHT: 0px; MARGIN-LEFT: 5px; MARGIN-RIGHT: 0px">
<DIV
style="FONT: 10pt arial; BACKGROUND: #e4e4e4; font-color: black"><B>From:</B>
<A title=susumu@mri.jhu.edu href="mailto:susumu@mri.jhu.edu">susumu mori</A>
</DIV>
<DIV style="FONT: 10pt arial"><B>To:</B> <A title=yj3@duke.edu
href="mailto:yj3@duke.edu">Yi Jiang</A> ; <A
title=mristudio-users@mristudio.org
href="mailto:mristudio-users@mristudio.org">DTI Studio, ROI Editor, Landmarker
Questions/Support</A> ; <A title=xli16@jhmi.edu
href="mailto:xli16@jhmi.edu">Xin Li</A> </DIV>
<DIV style="FONT: 10pt arial"><B>Sent:</B> Tuesday, July 14, 2009 2:21
AM</DIV>
<DIV style="FONT: 10pt arial"><B>Subject:</B> Re: [Mristudio-users] LDDMM
questions</DIV>
<DIV><BR></DIV>Hi Yi,<BR><BR>1) I recommend you to do AIR first from two
reasons. First one is a practical reason. Our LDDMM requires that the matrix
and pixel sizes of the two images are identical. After AIR, even if the input
images have different dimensions, the output will have the same dimension.
This is handy. Second one is more important. Let me use fitting of a X-Y plot
for analogy. When you use linear fitting, no matter which software you use,
the results are almost identical. This is because the energy landscape of
linear fitting usually has a very simple "one-valley" shape, meaning the
results always converge at the same solution. On the other hand, when you are
using non-linear fitting, you are required to provide initial values, which
are close to the real solution. Usually you first do linear solution and then
use the result as the initial value for the subsequent non-linear fitting.
This is because the energy landscape of non-linear fitting has a complicated
"multi-valley" shape. If your initial values are far away from the real
solution, the fitting is trapped by a local minima. <BR><BR>Non-linear warping
is very similar. You are required to bring two brains as close as possible
before you start non-linear warping.<BR><BR>When you adopt AIR+LDDMM, you have
to transform the image twice, including tensor reorientation. Landmarker can
combine transformation matrices so that you can do multiple transformation at
once to avoid multiple interpolation. <BR><BR>Xin, can we combine AIR matrix
and LDDMM matrix?<BR><BR>2) We usually don't use non-linear AIR. So we don't
have much experience with it. Yes, it should do tensor reorientation if you
apply the transformation to a tensor file.<BR><BR> <BR><BR>
<DIV class=gmail_quote>On Mon, Jul 13, 2009 at 4:12 PM, Yi Jiang <SPAN
dir=ltr><<A href="mailto:yj3@duke.edu">yj3@duke.edu</A>></SPAN>
wrote:<BR>
<BLOCKQUOTE
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class=gmail_quote>
<DIV bgcolor="#ffffff">
<DIV><FONT face=Arial>Dear All,</FONT></DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>I have two questions about
LDDMM:</FONT></DIV>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-FAMILY: Arial">1. if I have
a template image and a subject image and I want to register these two by
LDDMM eventually, 1). should I use LDDMM to register these two directly or
2). should I use AIR linear to affine transform them first, and then
LDDMM the updated subject image? In the 2<SUP>nd</SUP> case, I need to
reorient tensors twice, once by the AIR transformation matrix and once by
the LDDMM transformation matrix, right?</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-FAMILY: Arial">I am asking
this question because for some other registration software I have used, it
seems the elastic transformation works better after affine registering the
images first.</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-FAMILY: Arial">Or maybe
LDDMM covers rigid and affine transformation well already so we can do
#1?</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-FAMILY: Arial">2. How does
the nonlinear AIR compensate/compare with LDDMM? Can the nonlinear AIR
transformation be applied to reorient tensors?</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-FAMILY: Arial">Thank you
very much!</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial"></SPAN> </P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial">Best,</SPAN></P>
<P style="MARGIN: 0in 0in 0pt"><SPAN
style="FONT-FAMILY: Arial">Yi</SPAN></P></DIV><BR>_______________________________________________<BR>Mristudio-users
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