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, R0, T] = get_orient_info(avw);
0055     R = get_rot_from_orient(orient);
0056 else
0057     error('Orient is necessary for Analyze file ')
0058 end
0059 
0060 %if ftype == 0,
0061 %    % Flip x-asis for Analyze file (x+ : left)
0062 %    orient(1) = - orient(1);
0063 %end
0064 
0065 % --- change axis of image
0066 img = permute(avw.img, abs(orient));
0067 
0068 % orient = [3 1 2]
0069 % img(j3,j1,j2) = img(j1,j2,j3)
0070 
0071 dim = size(img);
0072 
0073 % --- flip image
0074 if orient(1) < 0
0075     img(1:dim(1),:,:) = img(dim(1):-1:1,:,:);
0076 end
0077 if orient(2) < 0
0078     img(:,1:dim(2),:) = img(:,dim(2):-1:1,:);
0079 end
0080 if orient(3) < 0
0081     img(:,:,1:dim(3)) = img(:,:,dim(3):-1:1);
0082 end
0083 
0084 avw.img = img;
0085 
0086 % --- change voxcel size & origin of image
0087 
0088 % [x ; y ; z] = R * [i ; j ; k] + T
0089 
0090 % No flip case
0091 % x = i + T1 (i=0:N1-1)
0092 %   = ii + X0 (ii=1:N1, X0=T1-1)
0093 % Flip case
0094 % x = -i + T1 (i=0:N1-1)
0095 % ii= N1 - i (ii=1:N1)
0096 % x = ii + X0 (ii=1:N1, X0=T1-N1)
0097 
0098 % originator
0099 % i0 = T1 (centor)
0100 % Flip case
0101 % ii = N1 - i
0102 % ii0 = N1 - i0 = N1 - T1
0103 
0104 if ftype == 1
0105     %  NIFTI data format
0106     vsize = hdr.dime.pixdim(2:4);
0107     vsize = abs(R * vsize(:));
0108     vox   = sum(R,2);
0109     vox = 0.5 * (1 - sign(vox));
0110     
0111     R = R0*R';
0112     T = T - R * (vox .* (dim(:) - 1));
0113     
0114     avw.hdr.hist.srow_x = [R(1,:) T(1)];
0115     avw.hdr.hist.srow_y = [R(2,:) T(2)];
0116     avw.hdr.hist.srow_z = [R(3,:) T(3)];
0117     
0118     avw.hdr.hist.originator(1:3) = - (T./vsize)';
0119     
0120 else
0121     %  Analyze data format
0122 %      hdr.hist.srow_x(1) = hdr.dime.pixdim(2);
0123 %      hdr.hist.srow_y(2) = hdr.dime.pixdim(3);
0124 %      hdr.hist.srow_z(3) = hdr.dime.pixdim(4);
0125 %      hdr.hist.srow_x(4) = (1-hdr.hist.originator(1))*hdr.dime.pixdim(2);
0126 %      hdr.hist.srow_y(4) = (1-hdr.hist.originator(2))*hdr.dime.pixdim(3);
0127 %      hdr.hist.srow_z(4) = (1-hdr.hist.originator(3))*hdr.dime.pixdim(4);
0128 %
0129     vsize = hdr.dime.pixdim(2:4);
0130     vsize = abs(R * vsize(:));
0131     vox   = sum(R,2);
0132 
0133     for j=1:3
0134         if  vox(j) > 0
0135             T(j) = T(j);
0136         else
0137             T(j) = dim(j) - T(j);
0138         end
0139     end
0140 
0141     avw.hdr.hist.srow_x = [1 0 0 -T(1)]*vsize(1);
0142     avw.hdr.hist.srow_y = [0 1 0 -T(2)]*vsize(2);
0143     avw.hdr.hist.srow_z = [0 0 1 -T(3)]*vsize(3);
0144     
0145     avw.hdr.hist.originator(1:3) = T';
0146 end
0147 
0148 avw.hdr.dime.dim(2:4) = dim;
0149 avw.hdr.dime.pixdim(2:4) = vsize';
0150 
0151 avw.hdr.hist.qform_code  = 0;
0152 avw.hdr.hist.sform_code  = 1;
0153 
0154 return
0155 
0156 %avw.
0157 %avw.
0158 %avw.
0159 
0160 % DIM     = avw.hdr.dime.dim(2:4)           % ²èÁü¥µ¥¤¥º
0161 % VOX     = avw.hdr.dime.pixdim(2:4)        % voxel¥µ¥¤¥º
0162 %
0163 % origin in voxcel-space -> origin in MNI-mm space
0164 %origin = vox(:) .* origin(:);
0165 %
0166 %Trans  = [vox(1) 0 0 -origin(1) ; ...
0167 %          0 vox(2) 0 -origin(2) ; ...
0168 %          0 0 vox(3) -origin(3) ; ...
0169 %          0 0      0    1     ];
0170 
0171 return