cor_img_read.m

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function [ avw, machine ] = cor_img_read(path,machine)

% COR_IMG_READ - Read Freesurfer format data (COR-001 to COR-256)
%
% [ avw, machine ] = cor_img_read(path, machine)
%
% path - the full path to the COR-??? image files.  If empty,
%        this function uses uigetfile to locate COR-???.
% 
% machine - a string, see machineformat in fread for details.
%           The default here is 'ieee-le' but the routine
%           will automatically switch between little and big
%           endian to read any such Analyze header.  It
%           reports the appropriate machine format and can
%           return the machine value.
%
% This function returns an Analyze data structure, with fields:
% 
% avw_hdr - a struct with image data parameters.
% avw_img - a 3D matrix of image data (double precision).
%
% See also: AVW_IMAGE_READ, AVW_HEADER_READ
%

% $Revision: 1.4 $ $Date: 2003/07/09 05:25:04 $

% Licence:  GNU GPL, no express or implied warranties
% History:  06/2002, [e-mail]
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


if ~exist('path','var'),
    fprintf('No input path - see help cor_img_read\n');
    [file, path] = uigetfile({'*.*'},'Select COR-001 File');
end
if ~exist('machine','var'), machine = 'ieee-le'; end

[path,name,ext] = fileparts(strcat(path,filesep,'COR-001'));
file = fullfile(path,[name ext]);
fid = fopen(file,'r',machine);

if fid < 0,
    fprintf('Cannot open file %s\n',file);
    fclose(fid);
else
    fclose(fid);
    avw = read_image(path,machine);
end

return

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ avw ] = read_image(path,machine)
    
    
    % Create the file header, 256^3, 1 mm^3, uchar, etc
    avw = avw_hdr_make;
    
    avw.hdr.dime.dim    =  int16([4 256 256 256 1 0 0 0]);
    avw.hdr.dime.pixdim = single([0   1   1   1 0 0 0 0]);
    
    PixelDim = double(avw.hdr.dime.dim(2));
    RowDim   = double(avw.hdr.dime.dim(3));
    SliceDim = double(avw.hdr.dime.dim(4));
    
    % Allocate memory for the image
    avw.img = zeros(PixelDim,SliceDim,RowDim);
    
    % Read one file/slice at a time
    for y = 1:SliceDim,
        
        file = sprintf('COR-%03d',y);
        fprintf('COR_IMAGE_READ:  Reading %s %s image.\n',machine,file);
        
        [path,name,ext] = fileparts(strcat(path,filesep,file));
        file = fullfile(path,[name ext]);
        
        % read the whole image into matlab (faster)
        fid = fopen(file,'r',machine); fseek(fid,0,'bof');
        tmp = fread(fid,inf,'uchar=>double');
        fclose(fid);
        
        % Arrange image into avw.img xyz matrix
        % For Freesurfer COR files the voxels are stored with
        % Pixels in 'x' axis (varies fastest) - from patient right to left
        % Rows in   'z' axis                  - from patient superior to inferior
        % Slices in 'y' axis                  - from patient posterior to anterior
        
        n = 1;
        for z = RowDim:-1:1,
            x = 1:PixelDim;
            avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
            n = n + PixelDim;
        end
    end
    
    
    avw.hdr.hist.orient = 0;
    
return