spm_get_orig_coord_spm5

=======================================================================
 Determine corresponding co-ordinate in un-normalised image.
 FORMAT orig_coord = get_orig_coord2(coord, matname,PU)
 coord      - [x1 y1 z1 ; x2 y2 z2 ; etc] in MNI space (mm).
 matname    - File containing transformation information (_sn.mat).
            - or the structure containing the transformation.
 PU         - Name of un-normalised image
 orig_coord - Co-ordinate in un-normalised image (voxel).

 FORMAT orig_coord = get_orig_coord2(coord, matname)
 coord      - [x1 y1 z1 ; x2 y2 z2 ; etc] in MNI space (mm).
 matname    - File containing transformation information (_sn.mat).
            - or the structure containing the transformation.
 orig_coord - Original co-ordinate (mm).
=======================================================================
 Copyright (C) 2005 Wellcome Department of Imaging Neuroscience

0001 function orig_coord = spm_get_orig_coord_spm5(coord, matname,PU)
0002 
0003 %=======================================================================
0004 % Determine corresponding co-ordinate in un-normalised image.
0005 % FORMAT orig_coord = get_orig_coord2(coord, matname,PU)
0006 % coord      - [x1 y1 z1 ; x2 y2 z2 ; etc] in MNI space (mm).
0007 % matname    - File containing transformation information (_sn.mat).
0008 %            - or the structure containing the transformation.
0009 % PU         - Name of un-normalised image
0010 % orig_coord - Co-ordinate in un-normalised image (voxel).
0011 %
0012 % FORMAT orig_coord = get_orig_coord2(coord, matname)
0013 % coord      - [x1 y1 z1 ; x2 y2 z2 ; etc] in MNI space (mm).
0014 % matname    - File containing transformation information (_sn.mat).
0015 %            - or the structure containing the transformation.
0016 % orig_coord - Original co-ordinate (mm).
0017 %=======================================================================
0018 % Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
0019 
0020 % John Ashburner
0021 % $Id: spm_get_orig_coord_spm5.m 1332 2011-02-24 06:57:20Z rhayashi $
0022 
0023 if ischar(matname)
0024     t = load(matname);
0025 elseif isstruct(matname)
0026     t = matname;
0027 else
0028     error('Wrong normalisation parameters!');
0029 end
0030     
0031 if size(coord,2)~=3, error('coord must be an N x 3 matrix'); end;
0032 coord = coord';
0033 
0034 Mat = inv(t.VG(1).mat);
0035 xyz = Mat(1:3,:)*[coord ; ones(1,size(coord,2))];
0036 Tr  = t.Tr;
0037 Affine = t.Affine;
0038 d   = t.VG(1).dim(1:3);
0039 
0040 if nargin>2,
0041     VU   = spm_vol(PU);
0042     Mult = VU.mat\t.VF.mat*Affine;
0043 %     disp('Output co-ordinates are in voxels');
0044 else
0045     Mult = t.VF.mat*Affine;
0046 %     disp('Output co-ordinates are in mm');
0047 end;
0048 
0049 if (prod(size(Tr)) == 0),
0050         affine_only = 1;
0051         basX = 0; tx = 0;
0052         basY = 0; ty = 0;
0053         basZ = 0; tz = 0;
0054 else,
0055         affine_only = 0;
0056         basX = spm_dctmtx(d(1),size(Tr,1),xyz(1,:)-1);
0057         basY = spm_dctmtx(d(2),size(Tr,2),xyz(2,:)-1);
0058         basZ = spm_dctmtx(d(3),size(Tr,3),xyz(3,:)-1);
0059 end;
0060 
0061 if affine_only,
0062     xyz2 = Mult(1:3,:)*[xyz ; ones(1,size(xyz,2))];
0063 else,
0064     xyz2 = zeros(3,size(xyz,2));
0065     for i=1:size(xyz,2),
0066         bx = basX(i,:);
0067         by = basY(i,:);
0068         bz = basZ(i,:);
0069         tx = reshape(...
0070             reshape(Tr(:,:,:,1),size(Tr,1)*size(Tr,2),size(Tr,3))...
0071             *bz', size(Tr,1), size(Tr,2) );
0072         ty = reshape(...
0073             reshape(Tr(:,:,:,2),size(Tr,1)*size(Tr,2),size(Tr,3))...
0074             *bz', size(Tr,1), size(Tr,2) );
0075         tz =  reshape(...
0076             reshape(Tr(:,:,:,3),size(Tr,1)*size(Tr,2),size(Tr,3))...
0077             *bz', size(Tr,1), size(Tr,2) );
0078         xyz2(:,i) = Mult(1:3,:)*[xyz(:,i) + [bx*tx*by' ; bx*ty*by' ; bx*tz*by']; 1];
0079     end;
0080 end;
0081 orig_coord = xyz2';
0082 
0083 return;