avw_img_compose.html

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0078     warning(msg);
0079     <span class="comment">% OK this field is probably FOV, so lets</span>
0080     <span class="comment">% divide it by the total number of slices</span>
0081     SliceFOV = double(avw.hdr.dime.pixdim(4));
0082     avw.hdr.dime.pixdim(4) = single(SliceFOV / Nfiles);
0083 <span class="keyword">end</span>
0084 
0085 <span class="comment">% Initialise avw.img and reset some header dimensions</span>
0086 avw.hdr.dime.dim(4) = Nfiles;
0087 avw = <a href="#_sub2" class="code" title="subfunction [avw] = avw_img_init(avw),">avw_img_init</a>(avw);
0088 
0089 <span class="comment">% Now reset orient field of avw, as all data will</span>
0090 <span class="comment">% be in standard axial unflipped orientation after</span>
0091 <span class="comment">% avw_img_read.</span>
0092 avw.hdr.hist.orient = char(0);
0093 
0094 
0095 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0096 <span class="comment">% Add slices, depends on whether slice order is normal or flipped</span>
0097 
0098 orient = double(firstslice.hdr.hist.orient);
0099 
0100 <span class="keyword">if</span> orient &lt; 3,
0101     <span class="comment">% process slices as unflipped volume</span>
0102     <span class="keyword">for</span> f = 1:Nfiles,
0103         <span class="keyword">if</span> files(f).bytes == Fsize,
0104             slice = <a href="avw_img_read.html" class="code" title="function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)">avw_img_read</a>(files(f).name,IMGorient,machine);
0105             avw   = <a href="#_sub1" class="code" title="subfunction [avw] = avw_add_slice(avw,slice,Nslice,orient),">avw_add_slice</a>(avw,slice,f,orient);
0106         <span class="keyword">else</span>
0107             msg = sprint(<span class="string">'AVW_IMG_COMPOSE: This file is not the same size as the first file!'</span>);
0108             error(msg);
0109         <span class="keyword">end</span>
0110     <span class="keyword">end</span>
0111 <span class="keyword">else</span>
0112     <span class="comment">% process slices as flipped volume</span>
0113     <span class="keyword">for</span> f = Nfiles:-1:1,
0114         <span class="keyword">if</span> files(f).bytes == Fsize,
0115             slice = <a href="avw_img_read.html" class="code" title="function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)">avw_img_read</a>(files(f).name,IMGorient,machine);
0116             avw   = <a href="#_sub1" class="code" title="subfunction [avw] = avw_add_slice(avw,slice,Nslice,orient),">avw_add_slice</a>(avw,slice,f,orient);
0117         <span class="keyword">else</span>
0118             msg = sprint(<span class="string">'AVW_IMG_COMPOSE: This file is not the same size as the first file!'</span>);
0119             error(msg);
0120         <span class="keyword">end</span>
0121     <span class="keyword">end</span>
0122 <span class="keyword">end</span>
0123 
0124 
0125 <span class="keyword">return</span>
0126 
0127 
0128 
0129 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0130 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0131 <a name="_sub1" href="#_subfunctions" class="code">function [avw] = avw_add_slice(avw,slice,Nslice,orient),</a>
0132     
0133     <span class="comment">% Check that composed volume and current slice</span>
0134     <span class="comment">% have the same orientation</span>
0135     Vorient = double(  avw.hdr.hist.orient);
0136     Sorient = double(slice.hdr.hist.orient);
0137     
0138     <span class="keyword">if</span> Vorient ~= Sorient,
0139         msg = sprintf(<span class="string">'AVW_IMG_COMPOSE: Slice %3d has different orientation to volume'</span>,Nslice);
0140         error(msg);
0141     <span class="keyword">end</span>
0142     
0143     <span class="keyword">switch</span> double(orient),
0144     
0145     <span class="keyword">case</span> 0, <span class="comment">% axial unflipped</span>
0146         
0147         <span class="comment">% Slices in 'z' axis - from patient inferior to superior</span>
0148         avw.img(:,:,Nslice) = slice.img;
0149         
0150     <span class="keyword">case</span> 1, <span class="comment">% coronal unflipped</span>
0151         
0152         <span class="comment">% Slices in 'y' axis - from patient posterior to anterior</span>
0153         avw.img(:,Nslice,:) = slice.img;
0154         
0155     <span class="keyword">case</span> 2, <span class="comment">% sagittal unflipped</span>
0156         
0157         <span class="comment">% Slices in 'x' axis - from patient right to left</span>
0158         avw.img(Nslice,:,:) = slice.img;
0159         
0160     <span class="keyword">case</span> 3, <span class="comment">% axial flipped</span>
0161         
0162         <span class="comment">% Slices in 'z' axis - from patient inferior to superior</span>
0163         avw.img(:,:,Nslice) = slice.img;
0164         
0165     <span class="keyword">case</span> 4, <span class="comment">% coronal flipped</span>
0166         
0167         <span class="comment">% Slices in 'y' axis - from patient anterior to posterior</span>
0168         avw.img(:,Nslice,:) = slice.img;
0169         
0170     <span class="keyword">case</span> 5, <span class="comment">% sagittal flipped</span>
0171         
0172         <span class="comment">% Slices in 'x' axis - from patient right to left</span>
0173         avw.img(Nslice,:,:) = slice.img;
0174     <span class="keyword">end</span>
0175     
0176 <span class="keyword">return</span>
0177 
0178 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0179 <a name="_sub2" href="#_subfunctions" class="code">function [avw] = avw_img_init(avw),</a>
0180     
0181     PixelDim = double(avw.hdr.dime.dim(2));
0182     RowDim   = double(avw.hdr.dime.dim(3));
0183     SliceDim = double(avw.hdr.dime.dim(4));
0184     
0185     PixelSz  = double(avw.hdr.dime.pixdim(2));
0186     RowSz    = double(avw.hdr.dime.pixdim(3));
0187     SliceSz  = double(avw.hdr.dime.pixdim(4));
0188     
0189     <span class="keyword">switch</span> double(avw.hdr.hist.orient),
0190     
0191     <span class="keyword">case</span> {0,3}, <span class="comment">% axial unflipped or flipped</span>
0192         
0193         x = PixelDim;   Xsz = PixelSz;
0194         y = RowDim;     Ysz = RowSz;
0195         z = SliceDim;   Zsz = SliceSz;
0196         
0197     <span class="keyword">case</span> {1,4}, <span class="comment">% coronal unflipped or flipped</span>
0198         
0199         x = PixelDim;   Xsz = PixelSz;
0200         y = SliceDim;   Ysz = SliceSz;
0201         z = RowDim;     Zsz = RowSz;
0202         
0203     <span class="keyword">case</span> {2,5}, <span class="comment">% sagittal unflipped or flipped</span>
0204         
0205         x = SliceDim;   Xsz = SliceSz;
0206         y = PixelDim;   Ysz = PixelSz;
0207         z = RowDim;     Zsz = RowSz;
0208         
0209     <span class="keyword">otherwise</span>, <span class="comment">% assume axial unflipped or flipped</span>
0210         
0211         msg = sprintf(<span class="string">'AVW_IMG_COMPOSE: No specified orientation\n'</span>);
0212         warning(msg);
0213         
0214         x = PixelDim;   Xsz = PixelSz;
0215         y = RowDim;     Ysz = RowSz;
0216         z = SliceDim;   Zsz = SliceSz;
0217         
0218     <span class="keyword">end</span>
0219     
0220     avw.img = zeros(x,y,z);
0221     avw.hdr.dime.dim(2) = x;
0222     avw.hdr.dime.dim(3) = y;
0223     avw.hdr.dime.dim(4) = z;
0224     
0225     avw.hdr.dime.pixdim(2) = Xsz;
0226     avw.hdr.dime.pixdim(3) = Ysz;
0227     avw.hdr.dime.pixdim(4) = Zsz;
0228     
0229 <span class="keyword">return</span></pre></div>
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