Image Processing & Filtering

Analyze Image

• Load image

vol = readanalyze('mri_test.hdr');

Cropping

• Workaround for out of memory error

vol2=vol(200:399,150:449,10:26);

Interpolation

• Interpolation on z axis to ease livewire segmentation (amt depends on size... may run out of memory)

interpAmt=0.4;
sizex=size(vol2,2);
sizey=size(vol2,1);
sizez=size(vol2,3);
[x,y,z] = meshgrid(1:sizex, 1:sizey, 1:sizez);
[xi,yi,zi] = meshgrid (1:sizex, 1:sizey, 1:interpAmt:sizez);
vi = interp3(x,y,z,vol2,xi,yi,zi,'linear');

Noise Reduction

• Non-linear diffusion

Sharpening

• High pass filter: subtract the low pass filter image from original data set

w=ones(3,3,3);
w(2,2,2)=-8;
% w=fspecial('laplacian',0);
w=im2double(w);
f2=im2double(vol2);
g2=imfilter(f2,w,'replicate');
new = f2-g2;

Brightness & Contrast

• Livewire tool

View Slice

figure;
imagesc(squeeze(vi(:,:,sizez)));
axis equal;
colormap gray;