00001 function [err,XYZdic] = AFNI_Index2XYZcontinuous (Indx, Info, CoordCode)
00002 %
00003 %   [err,XYZdic] = AFNI_Index2XYZcontinuous (Indx, Info, [CoordCode])
00004 %
00005 %Purpose:
00006 %   Change from voxel XYZindex (called Voxel Coords in AFNI) to XYZ in mm 
00007 %   The mm and voxel coordinates refer to the values displayed 
00008 %   on the top left corner of AFNI controller.
00009 %   CoordCode is the one you'd set from the Coord Order plugin
00010 %   
00011 %   
00012 %Input Parameters:
00013 %   Indx an Mx3 matrix or an  Mx1 vector containing the voxel indices to be
00014 %        transformed to voxel coordinates.  (indices start at 0)
00015 %   Info is the output of BrikInfo
00016 %   CoordCode is an optional parameter used to specify the coordinates system of the output
00017 %      if empty or not specified, the default is 'RAI'. The code can be either a string or a vector 
00018 %      of numbers (see AFNI_CoordChange for more on that)
00019 %
00020 %Output Parameters:
00021 %   err : 0 No Problem
00022 %       : 1 Mucho Problems
00023 %   XYZdic : The continuous coordinates corresponding to Indx
00024 %       The coordnate system output is in RAI (DICOM) 
00025 %       unless otherwise specified by CoordCode
00026 %   
00027 %      
00028 %Key Terms:
00029 %   
00030 %More Info :
00031 %   BrikInfo
00032 %   Test_AFNI_Index2XYZcontinuous
00033 %   AFNI_XYZcontinuous2Index
00034 %   Test_AFNI_XYZcontinuous2Index
00035 %
00036 %     Author : Ziad Saad
00037 %     Date : Tue Sep 5 21:48:06 PDT 2000           Latest Modification: Feb 18 04
00038 %     LBC/NIMH/ National Institutes of Health, Bethesda Maryland
00039 
00040 
00041 %Define the function name for easy referencing
00042 FuncName = 'AFNI_Index2XYZcontinuous';
00043 
00044 %Debug Flag
00045 DBG = 1;
00046 
00047 ChangeCoord = 0;
00048 if (nargin == 3)
00049         if (~isempty(CoordCode)),
00050                 ChangeCoord = 1;
00051         end   
00052 end
00053 
00054 
00055 %initailize return variables
00056 err = 1;
00057 XYZmm = [];
00058 
00059 %make sure Indx is the right size 
00060 switch size(Indx,2),
00061         case 1, %change 1D index to XYZ index
00062                 [err, Indx] = AfniIndex2AfniXYZ (Indx, Info.DATASET_DIMENSIONS(1), Info.DATASET_DIMENSIONS(2))
00063         case 3, %OK
00064         otherwise,
00065                 err = ErrEval(FuncName,'Err_Bad dimension for Indx');
00066                 return
00067 end
00068 
00069 XYZmm = Indx;
00070 
00071         %The equations that would change the indices to coordinate system result in a coordinate system that 
00072         % may be any permutation of RAI (like IRA or AIR or IAR or RIA or ARI) so one only needs to find the 
00073         %dimension permutation needed to bring the final result to RAI.
00074 
00075         %determine the ordering map to go from any permutation of RAI to RAI
00076                 %[maploc(1),jnk] = find(Info.Orientation == 'R');
00077                 %[maploc(2),jnk] = find(Info.Orientation == 'A');
00078                 %[maploc(3),jnk] = find(Info.Orientation == 'I');
00079         
00080         %pre - Wed May 23 18:20:56 PDT 2001 - WRONG !
00081                 %XYZmm(:, maploc(1)) = Info.ORIGIN(1) + Indx(:,1) .* Info.DELTA(1);
00082                 %XYZmm(:, maploc(2)) = Info.ORIGIN(2) + Indx(:,2) .* Info.DELTA(2);
00083                 %XYZmm(:, maploc(3)) = Info.ORIGIN(3) + Indx(:,3) .* Info.DELTA(3);
00084 
00085         %post - Wed May 23 18:20:56 PDT 2001 - WRONG! 
00086                 %XYZmm(:, 1) = Info.ORIGIN(maploc(1)) + Indx(:,maploc(1)) .* Info.DELTA(maploc(1));
00087                 %XYZmm(:, 2) = Info.ORIGIN(maploc(2)) + Indx(:,maploc(2)) .* Info.DELTA(maploc(2));
00088                 %XYZmm(:, 3) = Info.ORIGIN(maploc(3)) + Indx(:,maploc(3)) .* Info.DELTA(maploc(3));
00089         
00090    %Feb 18 04, back to the original
00091       XYZmm(:, 1) = Info.ORIGIN(1) + Indx(:,1) .* Info.DELTA(1);
00092                 XYZmm(:, 2) = Info.ORIGIN(2) + Indx(:,2) .* Info.DELTA(2);
00093                 XYZmm(:, 3) = Info.ORIGIN(3) + Indx(:,3) .* Info.DELTA(3);
00094       %Now this is in the axis orientation which is Info.Orientation(:,1)' called 3dmm in thd_coords.c
00095       [err,XYZdic, map] = THD_3dmm_to_dicomm (Info, XYZmm);
00096 
00097 if (ChangeCoord),
00098         [err, maplocation, mapsign, XYZdic] = AFNI_CoordChange ('RAI', CoordCode, XYZdic);
00099 end
00100 
00101 err = 0;
00102 return;
00103