change_orient_ras

 change_orientation
   [avw] = change_orient_ras(avw,orient)
 --- Input
 avw : NIFTI/Analyze data structure
 orient : axis dim to get RAS coordinate
        - necessary for Analyze
        - unnecessary for NIFTI
 --- orient
 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]
 --- sform transform
 i = 0 .. dim[1]-1
 j = 0 .. dim[2]-1
 k = 0 .. dim[3]-1
 x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
 y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
 z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
 --- matrix form
 [x ; y ; z] = R * [i ; j ; k] + T

  Part of this file is copied and modified under GNU license from
  NIFTI TOOLBOX developed by Jimmy Shen

 Made by Masa-aki Sato 2008-02-17

0001 function   [avw] = change_orient_ras(avw,orient)
0002 % change_orientation
0003 %   [avw] = change_orient_ras(avw,orient)
0004 % --- Input
0005 % avw : NIFTI/Analyze data structure
0006 % orient : axis dim to get RAS coordinate
0007 %        - necessary for Analyze
0008 %        - unnecessary for NIFTI
0009 % --- orient
0010 % orient : axis dim to get RAS coordinate
0011 %        = [orient_x  orient_y  orient_z]
0012 % orient_x : Left to Right axis dim of current image
0013 % orient_y : Posterior to Anterior axis dim of current image
0014 % orient_z : Inferior  to Superior  axis dim of current image
0015 %            current image axis dim is [+-1/+-2/+-3] for [+-x/+-y/+-z]
0016 % --- sform transform
0017 % i = 0 .. dim[1]-1
0018 % j = 0 .. dim[2]-1
0019 % k = 0 .. dim[3]-1
0020 % x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
0021 % y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
0022 % z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
0023 % --- matrix form
0024 % [x ; y ; z] = R * [i ; j ; k] + T
0025 %
0026 %  Part of this file is copied and modified under GNU license from
0027 %  NIFTI TOOLBOX developed by Jimmy Shen
0028 %
0029 % Made by Masa-aki Sato 2008-02-17
0030 
0031 
0032 hdr = avw.hdr;
0033 
0034 if isfield(avw,'filetype') & avw.filetype > 0
0035     %  NIFTI data format
0036     ftype = 1;
0037 else
0038     %  Analyze data format
0039     ftype = 0;
0040 end
0041 
0042 if exist('orient','var')
0043     R = get_rot_from_orient(orient);
0044 
0045     if ftype == 0
0046         %  Analyze data format
0047         T = hdr.hist.originator(1:3);
0048         T = abs( R * T(:) );
0049     else
0050         error('No orient is necessary for NIFTI file ')
0051     end
0052 elseif ftype == 1
0053     %  NIFTI data format
0054     % orient : axis dim to get RAS coordinate
0055     [orient, R0, T] = get_orient_info(avw);
0056     % rotation matrix from orient
0057     R = get_rot_from_orient(orient);
0058 else
0059     error('Orient is necessary for Analyze file ')
0060 end
0061 
0062 % --- change axis of image to RAS according to orient
0063 img = permute(avw.img, abs(orient));
0064 
0065 % orient = [3 1 2]
0066 % img(j3,j1,j2) = img(j1,j2,j3)
0067 
0068 dim = size(img);
0069 
0070 % --- flip image according to orient
0071 if orient(1) < 0
0072     img(1:dim(1),:,:) = img(dim(1):-1:1,:,:);
0073 end
0074 if orient(2) < 0
0075     img(:,1:dim(2),:) = img(:,dim(2):-1:1,:);
0076 end
0077 if orient(3) < 0
0078     img(:,:,1:dim(3)) = img(:,:,dim(3):-1:1);
0079 end
0080 
0081 % image with RAS orientation
0082 avw.img = img;
0083 
0084 % --- transform voxcel size
0085 vsize = hdr.dime.pixdim(2:4); % pixdim of original image
0086 vsize = abs(R * vsize(:));    % pixdim of transformed RAS image
0087 
0088 avw.hdr.dime.dim(2:4)    = dim;
0089 avw.hdr.dime.pixdim(2:4) = vsize';
0090 
0091 avw.hdr.hist.sform_code  = 1;
0092 
0093 % --- No translation of origine
0094 % --- sform transform
0095 % i = 0 .. dim[1]-1
0096 % j = 0 .. dim[2]-1
0097 % k = 0 .. dim[3]-1
0098 % x = srow_x[0] * i + srow_x[1] * j + srow_x[2] * k + srow_x[3]
0099 % y = srow_y[0] * i + srow_y[1] * j + srow_y[2] * k + srow_y[3]
0100 % z = srow_z[0] * i + srow_z[1] * j + srow_z[2] * k + srow_z[3]
0101 
0102 avw.hdr.hist.srow_x = [1 0 0 0]*vsize(1);
0103 avw.hdr.hist.srow_y = [0 1 0 0]*vsize(2);
0104 avw.hdr.hist.srow_z = [0 0 1 0]*vsize(3);
0105 
0106 % origine = image center
0107 % 0 = srow_x[0] * dim(1)/2 + srow_x[3]
0108 avw.hdr.hist.srow_x(4) = - avw.hdr.hist.srow_x(1) * dim(1)/2;
0109 avw.hdr.hist.srow_y(4) = - avw.hdr.hist.srow_y(2) * dim(2)/2;
0110 avw.hdr.hist.srow_z(4) = - avw.hdr.hist.srow_z(3) * dim(3)/2;
0111 
0112 avw.hdr.hist.originator(1:3) = 0;
0113 
0114 
0115 avw.hdr.hist.qform_code  = 0;
0116 
0117 avw.hdr.hist.quatern_b   = 0;
0118 avw.hdr.hist.quatern_c   = 0;
0119 avw.hdr.hist.quatern_d   = 0;
0120 avw.hdr.hist.qoffset_x   = 0;
0121 avw.hdr.hist.qoffset_y   = 0;
0122 avw.hdr.hist.qoffset_z   = 0;
0123 
0124 return
0125 
0126 %avw.
0127 %avw.
0128 %avw.
0129 
0130 % DIM     = avw.hdr.dime.dim(2:4)           % 画像サイズ
0131 % VOX     = avw.hdr.dime.pixdim(2:4)        % voxelサイズ
0132 %
0133 % origin in voxcel-space -> origin in MNI-mm space
0134 %origin = vox(:) .* origin(:);
0135 %
0136 %Trans  = [vox(1) 0 0 -origin(1) ; ...
0137 %          0 vox(2) 0 -origin(2) ; ...
0138 %          0 0 vox(3) -origin(3) ; ...
0139 %          0 0      0    1     ];
0140 
0141 return