function images = read_mrimage(dir_name, filter, w, h); 

% function images = read_mrimage(dir_name, filter, w, h); 
%
% Aug 2003, Farshad Moradi
% California Institute of Technology
%
% Reads analyze image file into matlab.
%
% Example:
%   cd E:\MRI\Experiments
%   images = read_mrimage('LE0002/raw_030618','*', 64, 64); 
%
% DICOM format can be converted to Analyze images 
% using MRIConvert (http://lcni.uoregon.edu/~jolinda/MRIConvert)
%
% Wildcards are allowed in filter
%
% To align the brain before reading the MRI data, use flirt:
%   drTransform3D.bat <input dir> <reference hdr file> 
% The batch file code is at the end of this file (as comment)
%


images = [];
fname = {};
dir_cont = dir([dir_name '/' filter '.img']);
for i=1:length(dir_cont),
    fname{i} = dir_cont(i).name;
end;
fname = sort(fname);
for i=1:length(fname),
    fid = fopen( [dir_name '/' fname{i}] );
    temp = fread(fid, 'short=>double');
    fclose(fid);
    images(i).name = fname{i};
    images(i).nslice = length(temp)/(w*h);
    images(i).data = reshape(temp, w, h, images(i).nslice);
    images(i).w = w;
    images(i).h = h;
end;
    

% % drTransform3D.bat:
%
% % @echo off
% % 
% % REM Usage:
% % REM  drTransfrom3D <input dir> <reference hdr file> 
% % REM
% % 
% % mkdir T_%1
% % for %%f in (%1\*.hdr) DO set tempfile=%%f
% % echo Calculating transfromation matrix using %tempfile%
% % flirt -in %tempfile% -ref %2 -dof 7 -omat T_%1.matrix
% % echo Applying transfromation
% % for %%f in (%1\*.hdr) DO flirt -in %%f -ref %2 -applyxfm -init T_%1.matrix -out T_%%f