<div dir="ltr">Hi all,<div><br></div><div>Thank you very much for all your suggestions! Just realize that ITK assuming a LPS coordinate, I need to invert all the image coordinate values to get right transformation matrix. Especially thanks to Alex and Luis's help!</div>
<div><br></div><div>However, the transformed result is still a little wrong: I found before and after resampling the image, the origin in the original image was a little shifted (centre of [0 0 0] point in original volume shifted to [x0, y0, z0], and this shifted value is different in upsample and downsample cases). What I exactly need for resampling is to have the centre of the origin pixel fixed.</div>
<div><br></div><div>Thank you very much!</div><div><br></div><div>Best,</div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Feb 19, 2014 at 2:05 PM, Alex Taylor <span dir="ltr"><<a href="mailto:Alex.Taylor@mathworks.com" target="_blank">Alex.Taylor@mathworks.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word">
<div>Hi,</div>
<div><br>
</div>
<div>I have a couple suggestions based on what you've told me.</div>
<div><br>
</div>
<ol>
<li>As Luis pointed out, ITK always performs resampling in a world coordinate system. You are discussing isotropic vs. non-isotropic voxels. It sounds to me like in ITK you may not be working in the default pixel based coordinate system and you are specifying
an original and spacing with your ITK images. If this is the case, you should look at the function IMWARP for resampling your images:</li></ol>
<div><a href="http://www.mathworks.com/help/images/ref/imwarp.html" target="_blank">http://www.mathworks.com/help/images/ref/imwarp.html</a></div>
<div><br>
</div>
<div>Using IMWARP, you can specify optional spatial referencing arguments along with your geometric transformation. These spatial referencing arguments define the position of the image grid in a world coordinate system, and are analogous to the Spacing/Origin
properties of the ITK image object.</div>
<div><br>
</div>
<div><a href="http://www.mathworks.com/help/images/ref/imref3dclass.html" target="_blank">http://www.mathworks.com/help/images/ref/imref3dclass.html</a></div>
<div><br>
</div>
<div>What I suspect is happening is that there is a difference in world units per pixel in your ITK images vs. your MATLAB images. If this is the case, you would expect that the "rotation matrix" portion of your transform would be consistent between ITK and
MATLAB but that your translation factors would be off by the difference in scale in each dimension between ITK and MATLAB. To confirm this, you should either register your images in ITK using an isotropic spacing of 1 unit/pixel in all dimensions to be consistent
with the default MATLAB coordinate system, or you should use IMWARP and define a world coordinate system when solving your registration/resampling that is consistent with the coordinate system in ITK. </div>
<div><br>
</div>
<div>2) I work on the Image Processing Toolbox and don't have very much experience at all with Neural Networks in MATLAB. I would recommend posting your second question to MATLAB Answers. MATLAB Answers is a very responsive forum and should provide you with
good information:</div>
<div><br>
</div>
<div><a href="http://www.mathworks.com/matlabcentral/answers/" target="_blank">http://www.mathworks.com/matlabcentral/answers/</a></div>
<div><br>
</div>
<div><u>- Alex</u></div>
<div><br>
</div>
<span>
<div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span>WANG Chengjia <<a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, February 18, 2014 11:13 PM<br>
<span style="font-weight:bold">To: </span>Alex Taylor <<a href="mailto:Alex.Taylor@mathworks.com" target="_blank">Alex.Taylor@mathworks.com</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [Insight-users] coordinate system<br>
</div><div><div class="h5">
<div><br>
</div>
<div>
<div>
<div dir="ltr">Hi Alex,
<div><br>
</div>
<div>Sorry to bother again, two additional questions as it is a very valuable chance to talk to a developer from the MathWorks. </div>
<div><br>
</div>
<div>1. Do you know how to get the same performance of Matlab function "interp3" in ITK so that I can control the number of slices I want to insert between two original slice?</div>
<div><br>
</div>
<div>2. The main reason I'm developing my present algorithm using c++ (ITK+OpenCV) is because of training of Radial basis neural network (NN). I found in Matlab, to train a NN, I have to put all the inputs in one matrix, then the NN training goes automatically
one iteration after another. But my problem is there are huge amount of NN inputs and I will encounter a memory overflow to complete the training process. So is there a way in Matlab to perform just one iteration of NN training?</div>
<div><br>
</div>
<div>Thank you very much for all your helps!</div>
<div><br>
</div>
<div>Best,</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Feb 19, 2014 at 4:00 AM, WANG Chengjia <span dir="ltr">
<<a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Alex,
<div><br>
</div>
<div>Thank you very much for fast response! </div>
<div><br>
</div>
<div>I'm using linear interpolation in both Matlab and ITK. It's strange that because the rotation matrix (used in transform->SetMatrix(rot)) was the same in both ITK and Matlab, I only need to x/y coordinate for translation (when doing trainsform->SetTranslation())
to get close result.</div>
<div><br>
</div>
<div>I've just realized that when I resample the data for isotropic voxels, ITK produced a few more slices, which may changed the Origin of the volume. Because in Matlab, the first slice in the original anisotropic volume is still the first slice in the interpolated
isotropic volume. But the result seems that in ITK this may not be true.</div>
<div>
<div><br>
</div>
<div>Thank you very much!</div>
<div><br>
</div>
<div>Best,</div>
</div>
<span><font color="#888888">
<div>Chengjia</div>
<div><br>
</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Wed, Feb 19, 2014 at 3:51 AM, Alex Taylor <span dir="ltr">
<<a href="mailto:Alex.Taylor@mathworks.com" target="_blank">Alex.Taylor@mathworks.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div>Hi Wang,</div>
<div><br>
</div>
<div>I'm a developer from the MathWorks who is also familiar with ITK. The x/y transpose issue is likely due to row major vs. column major differences between MATLAB and ITK. I'd have see the corresponding matlab and ITK code to say for sure.</div>
<div><br>
</div>
<div>When you resample your images in matlab/itk, which interpolation method are you using?</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Alex</div>
<div>
<div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
On Feb 18, 2014, at 10:41 PM, "WANG Chengjia" <<a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a>> wrote:<br>
<br>
</div>
<blockquote type="cite">
<div>
<div dir="ltr">More generally, I have a transformation matrix calculated, anyone know how to transform a volume using this matrix?
<div><br>
</div>
<div>It is just a simple Rigid 3D transformation. In Matlab, I just use "tform = maketform('affine', transM');" to make up the transformation and apply it using " tformarray " then the images are perfectly aligned. But in ITK, I find I have to switch the x,
y coordinate of translation when doing "targetTransform->SetTranslation(trans)". The result was still wrong, although quite close to the one I got in Matlab.</div>
<div><br>
</div>
<div>Can anyone help? Thanks in advance!</div>
<div><br>
</div>
<div>Best,</div>
<div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Feb 18, 2014 at 7:39 PM, WANG Chengjia <span dir="ltr">
<<a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello,
<div><br>
</div>
<div>I'm now working on a machine learning based 3D image registration work. To create the ground truth registration, I need to firstly using simple least square method to calculate a transformation from the corresponding point (I'm using RIRE datasets). </div>
<div><br>
</div>
<div>The same working flow in matlab and itk produced the same transformation matrix, but different transformed volume! In matlab, it's well aligned using the coordinates of control points given by RIRE dataset. But in ITK I have to inverse and switch the translation
parameters. Then I realized it's because of the different coordinate system in itk and Matlab. </div>
<div><br>
</div>
<div>Can anyone tell me a method to convert transformation matrix calculated from the common coordinate system into the ITK one?</div>
<div><br>
</div>
<div>Thank you very much!</div>
<div><br>
</div>
<div>Best,</div>
<span><font color="#888888">
<div>
<div><br>
</div>
-- <br>
Chengjia Wang<br>
Phd Student, <br>
University of Edinburgh<br>
Clinical Research Imaging Center (CRIC)<br>
Toshiba Medical Visualization Systems Europe, Ltd<br>
Email: <a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a><br>
</div>
</font></span></div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Chengjia Wang<br>
Phd Student, <br>
University of Edinburgh<br>
Clinical Research Imaging Center (CRIC)<br>
Toshiba Medical Visualization Systems Europe, Ltd<br>
Email: <a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a><br>
</div>
</div>
</blockquote>
</div>
</div>
<blockquote type="cite">
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</blockquote>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Chengjia Wang<br>
Phd Student, <br>
University of Edinburgh<br>
Clinical Research Imaging Center (CRIC)<br>
Toshiba Medical Visualization Systems Europe, Ltd<br>
Email: <a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a><br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
Chengjia Wang<br>
Phd Student, <br>
University of Edinburgh<br>
Clinical Research Imaging Center (CRIC)<br>
Toshiba Medical Visualization Systems Europe, Ltd<br>
Email: <a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a><br>
</div>
</div>
</div>
</div></div></span>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>Chengjia Wang<br>Phd Student, <br>University of Edinburgh<br>Clinical Research Imaging Center (CRIC)<br>Toshiba Medical Visualization Systems Europe, Ltd<br>Email: <a href="mailto:wangchengjia1986@gmail.com" target="_blank">wangchengjia1986@gmail.com</a><br>
</div>