You don't need to do all that. Just read it in as a 2D array initially. Here, see this snippet from my code:
% Read in image2D image data
% Get original, full-sized 2-D slice.
% Note: fread() requires that x_size and y_size be doubles.
% Note: fread() will return a 2D array if you pass in a 2D array for the number of bytes, as in [x_size y_size].
if stHeader.BytesPerVoxel == 1
oneSlice = fread(fileHandle, [x_size y_size], '*uint8');
elseif stHeader.BytesPerVoxel == 2
oneSlice = fread(fileHandle, [x_size y_size], '*int16'); % It will be a 2D array after this.
else
error('Unsupported BytesPerVoxel %d', stHeader.BytesPerVoxel);
end