spm_write_vol

 Write an image volume to disk, setting scales and offsets as appropriate
 FORMAT V = spm_write_vol(V,Y)
 V (input)  - a structure containing image volume information (see spm_vol)
 Y          - a one, two or three dimensional matrix containing the image voxels
 V (output) - data structure after modification for writing.
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 @(#)spm_write_vol.m    2.9 John Ashburner 03/02/26

0001 function V = spm_write_vol(V,Y)
0002 % Write an image volume to disk, setting scales and offsets as appropriate
0003 % FORMAT V = spm_write_vol(V,Y)
0004 % V (input)  - a structure containing image volume information (see spm_vol)
0005 % Y          - a one, two or three dimensional matrix containing the image voxels
0006 % V (output) - data structure after modification for writing.
0007 %_______________________________________________________________________
0008 % @(#)spm_write_vol.m    2.9 John Ashburner 03/02/26
0009 
0010 if ndims(Y)>3, error('Can only handle a maximum of 3 dimensions.'), end
0011 
0012 if ~isfield(V,'pinfo'), V.pinfo = [1,0,0]'; end
0013 
0014 dim = [size(Y) 1 1 1];
0015 if ~all(dim(1:3) == V.dim(1:3)) | (size(V.pinfo,2)~=1 & size(V.pinfo,2)~=dim(3)),
0016     error('Incompatible dimensions.');
0017 end
0018 
0019 
0020 % Set scalefactors and offsets
0021 %-----------------------------------------------------------------------
0022 dt = V.dim(4); if dt>256, dt = dt/256; end;
0023 if any(dt == [128+2 128+4 128+8]),
0024     % Convert to a form that Analyze will support
0025     dt = dt - 128;
0026 end;
0027 s            = find(dt == [2 4 8 128+2 128+4 128+8]);
0028 dmnmx        = [0 -2^15 -2^31 -2^7 0 0 ; 2^8-1 2^15-1 2^31-1 2^7-1 2^16 2^32];
0029 dmnmx        = dmnmx(:,s);
0030 V.pinfo(1,:) = 1;
0031 V.pinfo(2,:) = 0;
0032 mxs          = zeros(dim(3),1)+NaN;
0033 mns          = zeros(dim(3),1)+NaN;
0034 if ~isempty(s),
0035     for p=1:dim(3),
0036         tmp    = double(Y(:,:,p));
0037         tmp    = tmp(isfinite(tmp));
0038         if ~isempty(tmp),
0039             mxs(p) = max(tmp);
0040             mns(p) = min(tmp);
0041         end;
0042     end;
0043 
0044     if size(V.pinfo,2) ~= 1,
0045         for p=1:dim(3),
0046             mx = mxs(p);
0047             mn = mns(p);
0048             if ~isfinite(mx), mx = 0; end;
0049             if ~isfinite(mn), mn = 0; end;
0050             if mx~=mn,
0051                 V.pinfo(1,p) = (mx-mn)/(dmnmx(2)-dmnmx(1));
0052                 V.pinfo(2,p) = ...
0053                     (dmnmx(2)*mn-dmnmx(1)*mx)/(dmnmx(2)-dmnmx(1));
0054             else,
0055                 V.pinfo(1,p) = 0;
0056                 V.pinfo(2,p) = mx;
0057             end;
0058         end;
0059     else,
0060         mx = max(mxs(isfinite(mxs)));
0061         mn = min(mns(isfinite(mns)));
0062         if isempty(mx), mx = 0; end;
0063         if isempty(mn), mn = 0; end;
0064         if mx~=mn,
0065             V.pinfo(1,1) = (mx-mn)/(dmnmx(2)-dmnmx(1));
0066             V.pinfo(2,1) = (dmnmx(2)*mn-dmnmx(1)*mx)/(dmnmx(2)-dmnmx(1));
0067         else,
0068             V.pinfo(1,1) = 0;
0069             V.pinfo(2,1) = mx;
0070         end;
0071     end;
0072 end;
0073 
0074 %-Create and write image
0075 %-----------------------------------------------------------------------
0076 V = spm_create_vol(V);
0077 for p=1:V.dim(3),
0078     V = spm_write_plane(V,Y(:,:,p),p);
0079 end;
0080 V = spm_close_vol(V);