MATLAB: Loading a .vol file in matlab and display image

#.volImage Processing Toolbox

Hi; I have a .vol file, which is the raw data of a image that is a 3D binary file. The first three 32-bit values are integers defining the size of the volume along X, Y, and Z. These are followed by the raw data – unsigned 8-bit integers corresponding to intensity. I would like to load this data in matlab and display the 3d image but couldn't find the command related to .vol file format and haven't be able to reconstruct the image. please help me thanks,

Best Answer

See attached code for reading raw 3D image volumes. I have more data in my headers in yours so you'll have to adapt it to remove the lines that read the extra information that you don't have.

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MATLAB: Binary Stream into Matlab

Why are you reading it into a column when you want a 2D array? You can read directly into a 2D array. Here's a snippet from an m-file of mine:

oneSlice = fread(fileHandle, [x_size y_size], '*uint8');

Ok, then you have a 2D array. Not sure what your difficulty with imshow() is. You can simply do

imshow(oneSlice); % or whatever your matrix is called.

MATLAB: How to load a 3D volume image file (.vol extension) into MATLAB, edit individual 2D slices and save it back as a 3D image

From your information about the size of the volume and from the number of bytes in the file it would appear that it just contains the raw pixels encoded as 16-bit integers with absolutely nothing else, in particular, no information on the order of dimensions. A little bit of experimentation will be needed

fid = fopen('scan1.vol');
voxels = fread(fid, '*uint16');  %read as 16 bit unsigned. I'm assuming they're unsigned
fclose(fid);
voxels = reshape(voxels, [555, 556, 500]);  %you may need to permute the numbers here
%and you may need to permute the dimensions afterward

Best Answer

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MATLAB: Binary Stream into Matlab

MATLAB: How to load a 3D volume image file (.vol extension) into MATLAB, edit individual 2D slices and save it back as a 3D image

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