3D Reslicing using COMKAT image tool (basic)

Reslicing 3D image volume using COMKAT image tool (basic)

Overview

Reslicing a 3D (or 3D vs time) image dataset can be accomplished using the COMKAT image tool and sliceVolume(). This example explains how to create image slices from a volume in at a position, plane orientation, and magnification. The approach is to load the image volume dataset into an instance if an ImageVolumeData (abbreviated IVD) object and to use the sliceVolume() method.

Background

sliceVolume() is a mex-file written in c with an interface to MATLAB that makes the operation particularly efficient. COMKATImageTool uses sliceVolume() and you can use it too.

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Approach I. Demonstrate the method for coordinate transformations

Load a file using COMKAT image tool and use the functions to translate and rotate the image volume as you desire.

  ivd = ImageVolumeData();

Read data to ivd, e.g. read_DICOM()

  ivd = read_DICOM(ivd, pathName, fileName); % load volume into an instance of IVD object;

Create a list of indicies of all pixels in slice that we are creating

  [i, j] = meshgrid(0 : Nc-1, 0 : Nr-1);
   ij = [c(:)’ ; r(:)’];  % make matrix, each column corresponding to a single pixel in the slice we are creating

Specify the transformation matrix based on desired pixel spacing (zoom), position (location), orientation. ref [1] p. 275

  M = ( Insert the method for generating the transformation matrix );

Calculate physical (mm) location of each pixel in the desired slice

  xyz = M * ij;

Specify the reverse mapping matrix ( xyz --> index space of the original image volume )

  Mhat = ( Insert the method for generate the mapping);

Calculate voxel indcies into the volume corresponding to xyz physical location

  uvw =  Mhat * xyz;

Use sliceVolume() to interpolate the slice

  slice = sliceVolume(idv, v, u, w, backgroundPixelValue, ‘linear);

Display new slice

  figure, imagesc(slice); axis image % isotropic

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Approach II. Use coordinateGen() to do the coordinate transformation

• This should create same result as approach I but require fewer lines of coding since coordinateGen() does most things that are needed.

Read the image volume into an ImageVolumeData object

  ivd = ( Insert the method for reading data );

Use coordinateGen() to generate uvw

  [u, v, w] = coordinateGen(ivd, Nc, Nr, pixelSpacing, planePos, orientation); % Input the desired pixelSpacing, planePos and orientation matrices

Use sliceVolume() to interpolate

  slice = sliceVolume(idv, v, u, w, backgroundPixelValue, ‘linear);

Display slice

  figure, imagesc(slice); axis image % isotropic

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