change_orient_analyze

  Change orientation of analyze file image
    avw = change_orient_analyze(avw, orient_now)
    avw = change_orient_analyze(avw, orient_now, flip_sw)
 --- Input/output
 avw.hdr - a struct with image data parameters.
 avw.img - a 3D matrix of image data (double precision).
 orient_now : orient number of current image
 flip_sw : RAS or LAS switch
         = -1 : LAS [default]
         = +1 : RAS
 --- orient_now
 orient_now   = [orient_now_x  orient_now_y  orient_now_z]
 orient_now_x : current x-axis orient number defined below
 orient_now_y : current y-axis orient number defined below
 orient_now_z : current z-axis orient number defined below
 --- orient number
 Left to Right           1 [R]  % Right to Left          -1 [L]
 Posterior to Anterior   2 [A]  % Anterior to Posterior  -2 [P]
 Inferior to Superior    3 [S]  % Superior to Inferior   -3 [I]

 --- orient
   'orient_now' us transformed to 'orient' in the program
 orient : axis dim to get RAS coordinate
        = [orient_x  orient_y  orient_z]
 orient_x : Left to Right axis dim of current image
 orient_y : Posterior to Anterior axis dim of current image
 orient_z : Inferior  to Superior  axis dim of current image
            current image axis dim is [+-1/+-2/+-3] for [+-x/+-y/+-z]
 --- Example
 - ¸½ºß¤ÎºÂɸ¼´¤ÎÊý¸þ
 orient_now = [2 -3  1]; % x+: A , y+: I , z+: R   : AIR
 - RASºÂɸ¤ØÃÖ´¹
 orient     = [3  1 -2]; % z -> X, x -> Y, -y -> Z : RAS
  --- Permutation of axis
 img_RAS(j3,j1,j2) = img_now(j1,j2,j3)
  --- Flip axis
 img_RAS = img_RAS(:,:,N3:-1:1)

 Made by Masa-aki Sato 2008-02-17

0001 function   avw = change_orient_analyze(avw, orient_now, flip_sw)
0002 %  Change orientation of analyze file image
0003 %    avw = change_orient_analyze(avw, orient_now)
0004 %    avw = change_orient_analyze(avw, orient_now, flip_sw)
0005 % --- Input/output
0006 % avw.hdr - a struct with image data parameters.
0007 % avw.img - a 3D matrix of image data (double precision).
0008 % orient_now : orient number of current image
0009 % flip_sw : RAS or LAS switch
0010 %         = -1 : LAS [default]
0011 %         = +1 : RAS
0012 % --- orient_now
0013 % orient_now   = [orient_now_x  orient_now_y  orient_now_z]
0014 % orient_now_x : current x-axis orient number defined below
0015 % orient_now_y : current y-axis orient number defined below
0016 % orient_now_z : current z-axis orient number defined below
0017 % --- orient number
0018 % Left to Right           1 [R]  % Right to Left          -1 [L]
0019 % Posterior to Anterior   2 [A]  % Anterior to Posterior  -2 [P]
0020 % Inferior to Superior    3 [S]  % Superior to Inferior   -3 [I]
0021 %
0022 % --- orient
0023 %   'orient_now' us transformed to 'orient' in the program
0024 % orient : axis dim to get RAS coordinate
0025 %        = [orient_x  orient_y  orient_z]
0026 % orient_x : Left to Right axis dim of current image
0027 % orient_y : Posterior to Anterior axis dim of current image
0028 % orient_z : Inferior  to Superior  axis dim of current image
0029 %            current image axis dim is [+-1/+-2/+-3] for [+-x/+-y/+-z]
0030 % --- Example
0031 % - ¸½ºß¤ÎºÂɸ¼´¤ÎÊý¸þ
0032 % orient_now = [2 -3  1]; % x+: A , y+: I , z+: R   : AIR
0033 % - RASºÂɸ¤ØÃÖ´¹
0034 % orient     = [3  1 -2]; % z -> X, x -> Y, -y -> Z : RAS
0035 %  --- Permutation of axis
0036 % img_RAS(j3,j1,j2) = img_now(j1,j2,j3)
0037 %  --- Flip axis
0038 % img_RAS = img_RAS(:,:,N3:-1:1)
0039 %
0040 % Made by Masa-aki Sato 2008-02-17
0041 
0042 % avw = avw_img_read(fname);
0043 
0044 if ~exist('orient_now','var'), orient_now = [2 -3 1]; end;
0045 if ~exist('flip_sw','var'), flip_sw = -1; end; 
0046 
0047 orient = zeros(1,3);
0048 
0049 % Convert 'orient_now' to 'orient'
0050 for j=1:3
0051     ix = find( abs(orient_now) == j );
0052     orient(j) = ix * sign(orient_now(ix));
0053 end
0054 
0055 % Left/Right flip switch
0056 orient(1) = orient(1)*flip_sw;
0057 
0058 fprintf('Orient = [%d  %d  %d]\n', orient)
0059 
0060 %
0061 %  --- Change orientation of image
0062 %
0063 avw = change_orient_ras(avw , orient);
0064 
0065 return
0066 % --- sform transform
0067 % i = 0 .. dim[1]-1
0068 % j = 0 .. dim[2]-1
0069 % k = 0 .. dim[3]-1
0070 % x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
0071 % y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
0072 % z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
0073 % --- matrix form
0074 % [x ; y ; z] = R * [i ; j ; k] + T
0075 
0076 % No flip case
0077 % x = i + T1 (i=0:N1-1)
0078 %   = ii + X0 (ii=1:N1, X0=T1-1)
0079 % Flip case
0080 % x = -i + T1 (i=0:N1-1)
0081 % ii= N1 - i (ii=1:N1)
0082 % x = ii + X0 (ii=1:N1, X0=T1-N1)
0083 
0084 %dim = avw.hdr.dime.dim(2:4)
0085 %pixdim = avw.hdr.dime.pixdim(2:4)
0086 
0087 % DIM     = avw.hdr.dime.dim(2:4)           % ²èÁü¥µ¥¤¥º
0088 % VOX     = avw.hdr.dime.pixdim(2:4)        % voxel¥µ¥¤¥º
0089 % TYPE    = avw.hdr.dime.datatype           % data type
0090 % ORIGIN  = avw.hdr.hist.originator(1:3)    % ²èÁü¤Î¸¶ÅÀ