<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Dawood,<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">Hi Yann,
<div><br>
</div>
<div>Since you are using a mask for metric calculation I don't
think the </div>
<div>cause of your problem is the optimizer, I assume you are
using the</div>
<div>ImageMaskSpatialObject after segmenting part of your image
(?!!).</div>
</blockquote>
I'm quite sure the mask is the problem. I have good registration
results on the same wing except when I'm setting the moving mask
into the metric. Only in this case, the optimizer diverge. It
doesn't diverge when I set the fixed mask.<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>How do you initiate your mask? This can be tricky sometimes!</div>
</blockquote>
I first register the two B&W mask with amoeba optimizer, and
kappa metric. Then I transform the 2 B&W images to spatial
objects, and set them to the metric use to register my wings, with
the result of first registration as initialization.<br>
<br>
<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>I had a similar problem in the past, the origin of the image
mask </div>
<div>had a 256 pixles shift towards the center of the image, but
this was</div>
<div>only detectable when used in a Free Form Deformation due to
obvious</div>
<div>deformations induced only in the lower right corner of the
image! <br>
</div>
</blockquote>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>When I used the SpatialObjectToImageFilter to see whether if
my </div>
<div>mask was valid everything seemed fine but the results still
were wrong.</div>
<div>If this is your problem it can be solved by shifting the mask
towards</div>
<div>the origin of the image, a sample code for this would look
like the following,</div>
<div>
<div> SOTransformType::OffsetType originOffset;</div>
<div> originOffset[0] = -255;</div>
<div> originOffset[1] = -255;</div>
<div> maskSO->GetIndexToObjectTransform()->SetOffset(originOffset);</div>
</div>
</blockquote>
<br>
I've make sure that mask and images are in the same physical
coordinates. Registration works perfectly when I only change the
metric, and others optimizer, like one+one, are not diverging
(metric is decreasing, as I want). It really looks like It was a
derivative problem with moving mask ! <br>
<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>
<div><br>
</div>
</div>
<div>As for the LBFGSB optimizer you can read the following
papers,</div>
<div><span class="Apple-style-span" style="font-family:
Geneva,Arial,Helvetica,sans-serif; font-size: 14px;">
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">
[1] R. H. Byrd, P. Lu and J. Nocedal. <a
moz-do-not-send="true" class="el"
href="http://www.itk.org/Doxygen314/html/classA.html"
style="color: rgb(26, 65, 168); text-decoration: none;
font-weight: bold; ">A</a> Limited Memory Algorithm </p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">for
Bound Constrained Optimization, (1995), SIAM Journal on
Scientific </p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">
and Statistical Computing , 16, 5, pp. 1190-1208.</p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">[2]
C. Zhu, R. H. Byrd and J. Nocedal. L-BFGS-B: Algorithm 778: </p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">L-BFGS-B,
FORTRAN routines for large scale bound constrained </p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">optimization
(1997), ACM Transactions on Mathematical Software, <br>
</p>
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">
Vol 23, Num. 4, pp. 550 - 560.</p>
</span></div>
</blockquote>
After some try, I didn't manage to make this optimizer perform a
good registration. I'm using similarity transform, and the optimizer
does not support scaling, maybe it is one reason. <br>
But with a good initialization, and one+one optimizer, after
spending hours tweaking the parameters, I'm quite happy with the
result ! I wont get better with the metric I think !<br>
<br>
<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>HTH,<span class="Apple-style-span" style="font-family:
Geneva,Arial,Helvetica,sans-serif; font-size: 14px;">
<p style="font-family: Geneva, Arial, Helvetica, sans-serif; ">Dawood</p>
</span></div>
</blockquote>
<br>
Thanks a lot !<br>
<br>
<br>
Yann<br>
<br>
<br>
<br>
<br>
<br>
<br>
<blockquote
cite="mid:CAAbhdRuMbHMV3saLY8JimxUbFfpmTCwZN0vxbdtLkv4iTy8nWA@mail.gmail.com"
type="cite">
<div>
<div class="gmail_quote">On Mon, Jul 11, 2011 at 9:51 PM,
asertyuio <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:asertyuio@yahoo.fr">asertyuio@yahoo.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000"> Hy dawood, and thanks
for your interest !<br>
<br>
Because I did not found any solution to my divergence
problem, I did abandon the mutual information metric. I
try again today, and found what 'cause' the divergence.<br>
It comes only when I set a moving mask on the metric. No
problem with the fixed mask. Although, I'm sure of my mask
validity, because I'm doing an initialization with them,
and I've no problem with others metrics.<br>
<br>
I join a animated gif showing it. First step is mask
registration, second, image registration, with only a mask
on moving image. The metric value increase, despite the
optimizer is set to do the opposite.<br>
<br>
Setting both masks is important for me because I don't
want to take account of the background outlines on the
registration process.<br>
<br>
As I have mostly problems with the regular step gradient
optimizer, I think the problem must be related to
derivative computation in the metric, but I don't know.<br>
Could you confirm this ?<br>
<br>
I'm going to try the LBFGSB optimizer, but there is not
much information on it on itk user guide.<br>
<br>
Best regards,<br>
<br>
Yann<br>
<br>
Le 03/07/2011 19:59, Dawood Al Masslawi a écrit :
<blockquote type="cite">Yann,
<div><br>
</div>
<div>Apparently I misread your outputs, sorry :)</div>
<div><br>
</div>
<div>Have you tried other optimizers? LBFGSB optimizer
have proved to work well</div>
<div><br>
</div>
<div>with the Mattes MI.</div>
<div> <br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Dawood</div>
<div><br>
</div>
<div><br>
</div>
<div>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<</div>
<div><br>
</div>
<div>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<</div>
<div><br>
</div>
<div><span style="font-family:'Times New
Roman';font-size:medium">
<pre>Hi Yann,
If your initialized transform is precise (near perfect?!!) it's only natural
that the optimizer would change less. Have you tried to set the minimum
step length to a higher value?
In the example you provided the metric value is decreasing, isn't that
what you want?
Your fixed and moving images and their intensity distribution also can
effect the quality of the registration, it might be helpful to give us more
information about your images.
HTH,
Dawood
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><i><<<<<<<<<<<<<<<<<<<<<<<<<<<<<
</i>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><i><<<<<<<<<<<<<<<<<<<<<<<<<<<<<
</i>
Hi all,
I'm exploring the mattes mutual information metric with the similarity
transform. I have big problems with the regular step gradient optimizer.
First one, I initialize the transform quite precisely, so only small
change are required, especially for scale and rotation. But I must put
the scaling factor to 100 000, for a maximal step length of 2 to obtain
change around 0.01 for each step. Why is there a x100 between 2/100 000
(what I expect to be the scaled step length) and the one which really
append ?
Second one, the optimizer fails to minimize the metrics (the value seems
to increase), despite the fact that minimizeOn is set, and that I see a
clear behavior difference when maximizeOn is set.
I've played a lot with parameters without significant improvement.
Here is an example :
0 -0.0794786 [1.08213, 0.215013, 142.753, 93.1165, 19.484, -5.38814]
1 -0.0837397 [1.09388, 0.224094, 142.734, 93.1303, 21.0015, -4.08564]
2 -0.0781118 [1.10518, 0.231022, 142.713, 93.1446, 22.5308, -2.79707]
3 -0.07013 [1.11679, 0.230021, 142.688, 93.1515, 23.5889, -1.10016]
4 -0.060149 [1.13054, 0.220847, 142.661, 93.1574, 24.6365, 0.603225]
5 -0.0533438 [1.15086, 0.197135, 142.637, 93.1682, 26.0843, 1.98246]
6 -0.0552559 [1.16682, 0.181277, 142.611, 93.1705, 27.2256, 3.62452]
7 -0.0499306 [1.17806, 0.163796, 142.586, 93.1626, 27.8154, 5.53527]
8 -0.0436633 [1.18673, 0.144479, 142.567, 93.1464, 27.8202, 7.53499]
9 -0.0373628 [1.19785, 0.129059, 142.55, 93.1295, 27.8735, 9.53404]
10 -0.0307262 [1.21034, 0.0999255, 142.53, 93.1149, 28.3516, 11.4756]
11 -0.0280043 [1.21907, 0.0717341, 142.518, 93.0946, 28.3674, 13.4752]
12 -0.0261761 [1.22857, 0.0535265, 142.507, 93.0742, 28.5985, 15.4616]
13 -0.0226728 [1.23642, 0.0331298, 142.5, 93.0514, 28.5777, 17.4612]
14 -0.022181 [1.24189, 0.0185733, 142.495, 93.0282, 28.7283, 19.4553]
15 -0.0190938 [1.25188, -0.00835667, 142.492, 93.0041, 28.7346, 21.455]
16 -0.0196048 [1.25686, -0.0400155, 142.497, 92.9792, 28.4755, 23.4377]
17 -0.0188159 [1.2638, -0.0595771, 142.508, 92.9557, 27.975, 25.3738]
18 -0.0174128 [1.27541, -0.0936444, 142.496, 92.9314, 29.3307, 26.8434]
I've done a deep analysis of the metrics value on my images, and it
is very regular, so the gradient approach seems to be good. The global
minimum with exhaustive search is good also.
I try the 1+1 evo optimizer, he is doing much better, but do not reach
the desired minimum.
I really don't understand where does this behaviour comes from !
Does anyone have any idea of the step I could have missed up ?
Thanks in advance,
Regards,
Yann
</pre>
</span></div>
</blockquote>
</div>
</blockquote>
</div>
</div>
</blockquote>
<br>
</body>
</html>