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. Demonstrates 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();

Use 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

(set up coordinate transform for desired slice) ref p 275

  M = ( Insert the method for generate the transformation );

User specifies this based on desired pixel spacing (aka zoom), position (location), orientation

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

  xyz = M * ij;

this documents physical location voxels in the volume

  Mhat = ( transform for the stored volume )

Calculate voxe indcies into the volume corresponding to xyz physical location

  uvw =  ( Insert the method for calculating voxel indices );.

Use sliceVolume(.) to interpolate the results

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

Display slice

  figure, imagesc(slice); axis image % isotropic

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Approach II. Uses coordinateGen to do the coordinate transformation)

this should create same result as approach 1 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, orientationInput);

Use sliceVolume(.) to interpolate

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

Display slice

  figure, imagesc(slice); axis image % isotropic

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