Student Center

Solution: Load MRI images into MATLAB

%1
%Load mri.mat file
load mri;
%note the variables that are now loaded into the
%workspace: D, map, siz

%2
%Display all of the frames in one figure
figure
montage(D, map)
title('MRI Slices')


%3
%Isolate frame 5 and display in individual figure
%Movies in MATLAB are typically represented with four
%dimensions. The first and second dimensions are
%spatial (i.e. the vertical and horizontal axes as
%seen by any one image of the movie.) The third
%dimension is the color dimension with a size of one
%because it indexes into the colormap. The fourth
%dimension is temporal. Dimensions 1, 2, and 4 for
%this example are as follows:

• Dimension 1: Front to back of head (rostral/anterior to caudal/posterior)
• Dimension 2: Left to right of head
• Dimension 4: Bottom to top of head (inferior to superior)

%Therefore, to isolate frame 5, we use the fourth
%dimension.
frame_5=D(:,:,:,5);
figure
imshow(frame_5, map)
title('Frame 5 of MRI data')

%4
%Show all frames of MRI data as a movie
figure
immovie(D, map)

%5
%Obtain sagittal slice image of brain and show as
%individual image.

%The sagittal slice is a 2-D image showing the image
%from the bottom to %top of the head
%(inferior to superior) and front to back of the head
%(rostral/anterior to caudal/posterior).
%In this example, these two dimensions are the 1st and %4th dimension as described above.
%Therefore, D is now a 128 x 128 x 1 x 27 variable. We %want to take one slice of the brain (or one frame of
%the movie) and transform it using the 1st and 4th
%dimension.

%There are two functions you can use: imtransform,
%tformarray

%Limit one dimension of 4-D data to 1 point (Here,
%randomly selecting to limit second dimension and
%isolating 60th entry)
slice=D(:,60,:,:);
size_slice=size(slice)

%MATLAB will return:
size_slice =
128   1   1   27

%slice variable is now 128x1x1x27.
%make 4-D matrix into 2-D matrix (could also use
%SQUEEZE function)

slice2=reshape(slice, [128 27]);
size_slice2=size(slice2)

%MATLAB will return:
size_slice2 =
128    27

%construct transform to change horizontal view into
%sagittal view
T=maketform('affine',[0 -2.5; 1 0; 0 0]);
slice3=imtransform(slice2, T,'cubic');

%view as individual figure
figure
imshow(slice3, map)
title('Sagittal Slice')