xform_nii.m

Please read your package and describe it at least 40 bytes. System will automatically delete the di

   affine_transform = 1;

   %  NIFTI can have both sform and qform transform. This program
   %  will check sform_code prior to qform_code by default.
   %
   %  If user specifys "preferredForm", user can then choose the
   %  priority.					- Jeff
   %
   useForm=[];					% Jeff

   if isequal(preferredForm,'S')
       if isequal(hdr.hist.sform_code,0)
           error('User requires sform, sform not set in header');
       else
           useForm='s';
       end
   end						% Jeff

   if isequal(preferredForm,'Q')
       if isequal(hdr.hist.qform_code,0)
           error('User requires sform, sform not set in header');
       else
           useForm='q';
       end
   end						% Jeff

   if isequal(preferredForm,'s')
       if hdr.hist.sform_code > 0
           useForm='s';
       elseif hdr.hist.qform_code > 0
           useForm='q';
       end
   end						% Jeff
   
   if isequal(preferredForm,'q')
       if hdr.hist.qform_code > 0
           useForm='q';
       elseif hdr.hist.sform_code > 0
           useForm='s';
       end
   end						% Jeff

   if isequal(useForm,'s')
      R = [hdr.hist.srow_x(1:3)
           hdr.hist.srow_y(1:3)
           hdr.hist.srow_z(1:3)];

      T = [hdr.hist.srow_x(4)
           hdr.hist.srow_y(4)
           hdr.hist.srow_z(4)];

      if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
         hdr.hist.old_affine = [ [R;[0 0 0]] [T;1] ];
         R_sort = sort(abs(R(:)));
         R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
         hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];

         if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
            msg = [char(10) char(10) '   Non-orthogonal rotation or shearing '];
            msg = [msg 'found inside the affine matrix' char(10)];
            msg = [msg '   in this NIfTI file. You have 3 options:' char(10) char(10)];
            msg = [msg '   1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
            msg = [msg '      file. I strongly recommand this, because it will not cause' char(10)];
            msg = [msg '      negative effect, as long as you remember not to do slice' char(10)];
            msg = [msg '      time correction after using ''reslice_nii.m''.' char(10) char(10)];
            msg = [msg '   2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
            msg = [msg '      without applying any affine geometric transformation or' char(10)];
            msg = [msg '      voxel intensity scaling. This is only for people who want' char(10)];
            msg = [msg '      to do some image processing regardless of image orientation' char(10)];
            msg = [msg '      and to save data back with the same NIfTI header.' char(10) char(10)];
            msg = [msg '   3. Increasing the tolerance to allow more distortion in loaded' char(10)];
            msg = [msg '      image, but I don''t suggest this.' char(10) char(10)];
            msg = [msg '   To get help, please type:' char(10) char(10) '   help reslice_nii.m' char(10)];
            msg = [msg '   help load_untouch_nii.m' char(10) '   help load_nii.m'];
            error(msg);
         end
      end

   elseif isequal(useForm,'q')
      b = hdr.hist.quatern_b;
      c = hdr.hist.quatern_c;
      d = hdr.hist.quatern_d;

      if 1.0-(b*b+c*c+d*d) < 0
         if abs(1.0-(b*b+c*c+d*d)) < 1e-5
            a = 0;
         else
            error('Incorrect quaternion values in this NIFTI data.');
         end
      else
         a = sqrt(1.0-(b*b+c*c+d*d));
      end

      qfac = hdr.dime.pixdim(1);
      i = hdr.dime.pixdim(2);
      j = hdr.dime.pixdim(3);
      k = qfac * hdr.dime.pixdim(4);

      R = [a*a+b*b-c*c-d*d     2*b*c-2*a*d        2*b*d+2*a*c
           2*b*c+2*a*d         a*a+c*c-b*b-d*d    2*c*d-2*a*b
           2*b*d-2*a*c         2*c*d+2*a*b        a*a+d*d-c*c-b*b];

      T = [hdr.hist.qoffset_x
           hdr.hist.qoffset_y
           hdr.hist.qoffset_z];

      %  qforms are expected to generate rotation matrices R which are
      %  det(R) = 1; we'll make sure that happens.
      %  
      %  now we make the same checks as were done above for sform data
      %  BUT we do it on a transform that is in terms of voxels not mm;
      %  after we figure out the angles and squash them to closest 
      %  rectilinear direction. After that, the voxel sizes are then
      %  added.
      %
      %  This part is modified by Jeff Gunter.
      %
      if det(R) == 0 | ~isequal(R(find(R)), sum(R)')

         %  det(R) == 0 is not a common trigger for this ---
         %  R(find(R)) is a list of non-zero elements in R; if that
         %  is straight (not oblique) then it should be the same as 
         %  columnwise summation. Could just as well have checked the
         %  lengths of R(find(R)) and sum(R)' (which should be 3)
         %
         hdr.hist.old_affine = [ [R * diag([i j k]);[0 0 0]] [T;1] ];
         R_sort = sort(abs(R(:)));
         R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
         R = R * diag([i j k]);
         hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];

         if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
            msg = [char(10) char(10) '   Non-orthogonal rotation or shearing '];
            msg = [msg 'found inside the affine matrix' char(10)];
            msg = [msg '   in this NIfTI file. You have 3 options:' char(10) char(10)];
            msg = [msg '   1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
            msg = [msg '      file. I strongly recommand this, because it will not cause' char(10)];
            msg = [msg '      negative effect, as long as you remember not to do slice' char(10)];
            msg = [msg '      time correction after using ''reslice_nii.m''.' char(10) char(10)];
            msg = [msg '   2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
            msg = [msg '      without applying any affine geometric transformation or' char(10)];
            msg = [msg '      voxel intensity scaling. This is only for people who want' char(10)];
            msg = [msg '      to do some image processing regardless of image orientation' char(10)];
            msg = [msg '      and to save data back with the same NIfTI header.' char(10) char(10)];
            msg = [msg '   3. Increasing the tolerance to allow more distortion in loaded' char(10)];
            msg = [msg '      image, but I don''t suggest this.' char(10) char(10)];
            msg = [msg '   To get help, please type:' char(10) char(10) '   help reslice_nii.m' char(10)];
            msg = [msg '   help load_untouch_nii.m' char(10) '   help load_nii.m'];
            error(msg);
         end

      else
         R = R * diag([i j k]);
      end					% 1st det(R)

   else
      affine_transform = 0;	% no sform or qform transform
   end

   if affine_transform == 1
      voxel_size = abs(sum(R,1));
      inv_R = inv(R);
      originator = inv_R*(-T)+1;
      orient = get_orient(inv_R);

      %  modify pixdim and originator
      %
      hdr.dime.pixdim(2:4) = voxel_size;
      hdr.hist.originator(1:3) = originator;

      %  set sform or qform to non-use, because they have been
      %  applied in xform_nii
      %
      hdr.hist.qform_code = 0;
      hdr.hist.sform_code = 0;
   end

   %  apply space_unit to pixdim if not 1 (mm)
   %
   space_unit = get_units(hdr);

   if space_unit ~= 1
      hdr.dime.pixdim(2:4) = hdr.dime.pixdim(2:4) * space_unit;

      %  set space_unit of xyzt_units to millimeter, because
      %  voxel_size has been re-scaled
      %
      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,1,0));
      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,2,1));
      hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,3,0));
   end

   return;					% change_hdr


%-----------------------------------------------------------------------
function orient = get_orient(R)

   orient = [];

   for i = 1:3
      switch find(R(i,:)) * sign(sum(R(i,:)))
      case 1
         orient = [orient 1];		% Left to Right
      case 2
         orient = [orient 2];		% Posterior to Anterior
      case 3
         orient = [orient 3];		% Inferior to Superior
      case -1
         orient = [orient 4];		% Right to Left
      case -2
         orient = [orient 5];		% Anterior to Posterior
      case -3
         orient = [orient 6];		% Superior to Inferior
      end
   end

   return;					% get_orient


%-----------------------------------------------------------------------
function [space_unit, time_unit] = get_units(hdr)

   switch bitand(hdr.dime.xyzt_units, 7)	% mask with 0x07
   case 1
      space_unit = 1e+3;		% meter, m
   case 3
      space_unit = 1e-3;		% micrometer, um
   otherwise
      space_unit = 1;			% millimeter, mm
   end

   switch bitand(hdr.dime.xyzt_units, 56)	% mask with 0x38
   case 16
      time_unit = 1e-3;			% millisecond, ms
   case 24
      time_unit = 1e-6;			% microsecond, us
   otherwise
      time_unit = 1;			% second, s
   end

   return;					% get_units