MATLAB: 3D input parameters using imregister

imageImage Processing Toolboxregistration

Hi,

I would like to use imregister for registration of a volume. My data is MR images, so my volume is formed by 28 slices (my matrix is 512x512x28 int16). So my question is how should I pass this matrix as input using imregister? in both examples the input images are given as a simple 2D images, so I don't know how to use it for 3D, can someone help me?

Thank you in advance.

Best Answer

Hi Isabel,

You pass in a three dimensional image volume the same way you pass in a two dimensional image. Here is an example:

load mri;
D = padarray(squeeze(D),[5 5 5]);   %make bigger
D2 = imtranslate(D,[2.7 -5.1 1.5]); %Translate the image a little bit so imregister has to work
[optim metric]= imregconfig('monomodal');   %build the optimizer
mr = imregister(D2,D,'rigid',optim,metric); %register

imtranslate can be found here.

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Basically, then you're saying you want the registration algorithm to give more priority to the prostate alignment than to the rest of the anatomy? The only thing I can think of is that you might try to crop MR1 and MR2 to a smaller general region of the prostate, if you know it. If the prostate anatomy dominates the images, it will obviously get a lot of priority.

MATLAB: Problem with “imregister” function

Because imregister works with volumetric input as well as with planar 2-D images, there is ambiguity with multi-channel 2-D images, like your RGB input image.

To avoid this ambiguity, you need to form a 2-D image from your RGB image prior to calling imregister. One way to do this is to use rgb2gray on your moving and fixed images prior to calling imregister:

 fixed  = rgb2gray(fixed);
 moving = rgb2gray(moving);

You could also use a particular color channel, as ImageAnalyst suggested.

Otherwise, imregister is going to interpret your input imagery as a 3-plane volume. The error message you are getting is telling you that with the default number of PyramidLevels, there aren't enough pixels along the 3rd dimension to form a pyramid.

Best Answer

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