ge_series2avw.html

mri_toolbox是一个工具用来MRI. 来自于SourceForge, 我上传这个软件,希望能结识对医疗软件感兴趣的兄弟.

0087 
0088 <span class="comment">% Write the Analyze files (not doing this)</span>
0089 <span class="comment">%avw_write(avw,outName);</span>
0090 
0091 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0092 <span class="comment">% This is the original write code, now replace with above (DLW)...</span>
0093 
0094 <span class="comment">%outFile = strcat(outName,'.hdr');</span>
0095 <span class="comment">%status = ge_writeSPMHeader(outFile,header);</span>
0096 <span class="comment">%outFile = [outName sprintf('.img')];</span>
0097 <span class="comment">%[fid,message] = fopen(outFile,'w');</span>
0098 <span class="comment">%if (fid == -1),</span>
0099 <span class="comment">%    fprintf('Cannot Open %s for writing.\n',outFile);</span>
0100 <span class="comment">%    error(message);</span>
0101 <span class="comment">%end</span>
0102 <span class="comment">%fwrite(fid,reshape(imageVol,1,prod(size(imageVol))),'int16');</span>
0103 <span class="comment">%status = fclose(fid);</span>
0104 
0105 t=toc; fprintf(<span class="string">'...done (%5.2f sec).\n'</span>,t);
0106 
0107 <span class="keyword">return</span>
0108 
0109 
0110 
0111 
0112 
0113 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0114 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>
0115 
0116 <a name="_sub1" href="#_subfunctions" class="code">function [avw] = ge_reorient(ge, avw)</a>
0117 
0118 <span class="comment">%ge_reorient - Assigns Analyze header dimensions and volume based on GE orientation</span>
0119 <span class="comment">%</span>
0120 <span class="comment">% avw = ge_reorient(ge, avw)</span>
0121 <span class="comment">%</span>
0122 <span class="comment">% reorients the GE 3D volume to be radiological</span>
0123 <span class="comment">% orientation (axial LAS, which is SPM compatible)</span>
0124 <span class="comment">% based on the GE acquition orientation</span>
0125 <span class="comment">%</span>
0126 <span class="comment">% This has been tested with Ax,Sag,Cor with slices going</span>
0127 <span class="comment">% both ways.  Also for Oblique axial. Don't count on double</span>
0128 <span class="comment">% obliques or anything really fancy.</span>
0129 <span class="comment">%</span>
0130 
0131 
0132 <span class="comment">% Have looked over this orientation code carefully (DLW, 03/2003)</span>
0133 <span class="comment">% The above comments are from a previous version, note it</span>
0134 <span class="comment">% should be LAS, not RAS !!!!  I have found some inconsistencies</span>
0135 <span class="comment">% in the code (03/2003) and fixed it as best I can for now.  Further</span>
0136 <span class="comment">% testing with various volumes is required.</span>
0137 
0138 
0139 series_description = deblank(char(ge.hdr.series.se_desc)'); <span class="comment">% unreliable!</span>
0140 
0141 fprintf(<span class="string">'...checking GE series data orientation.\n'</span>);
0142 
0143 <span class="comment">% Determine the GE orientation</span>
0144 <span class="comment">% orient is 1=axial, 2=sagittal, 3=coronal</span>
0145 <span class="comment">% with opposite sign if backwards slice order</span>
0146 ras_start = char(ge.hdr.series.start_ras);
0147 ras_end   = char(ge.hdr.series.end_ras);
0148 <span class="keyword">if</span>     strcmp(ras_start,<span class="string">'I'</span>) &amp; strcmp(ras_end,<span class="string">'S'</span>),
0149     fprintf(<span class="string">'...slices are axial from inferior to superior.\n'</span>);
0150     orient =  1;
0151 <span class="keyword">elseif</span> strcmp(ras_start,<span class="string">'S'</span>) &amp; strcmp(ras_end,<span class="string">'I'</span>),
0152     fprintf(<span class="string">'...slices are axial from superior to inferior.\n'</span>);
0153     orient = -1;
0154 <span class="keyword">elseif</span> strcmp(ras_start,<span class="string">'R'</span>) &amp; strcmp(ras_end,<span class="string">'L'</span>),
0155     fprintf(<span class="string">'...slices are sagittal from right to left.\n'</span>);
0156     orient =  2;
0157 <span class="keyword">elseif</span> strcmp(ras_start,<span class="string">'L'</span>) &amp; strcmp(ras_end,<span class="string">'R'</span>),
0158     fprintf(<span class="string">'...slices are sagittal from left to right.\n'</span>);
0159     orient = -2;
0160 <span class="keyword">elseif</span> strcmp(ras_start,<span class="string">'P'</span>) &amp; strcmp(ras_end,<span class="string">'A'</span>),
0161     fprintf(<span class="string">'...slices are coronal from posterior to anterior.\n'</span>);
0162     orient =  3;
0163 <span class="keyword">elseif</span> strcmp(ras_start,<span class="string">'A'</span>) &amp; strcmp(ras_end,<span class="string">'P'</span>),
0164     fprintf(<span class="string">'...slices are coronal from anterior to posterior.\n'</span>);
0165     orient = -3;
0166 <span class="keyword">else</span>,
0167     warning(<span class="string">'GE orientation unknown!'</span>);
0168     orient = 0;
0169 <span class="keyword">end</span>
0170 
0171 <span class="comment">% Get the GE dimensions</span>
0172 nX = ge.hdr.image.imatrix_X;
0173 nY = ge.hdr.image.imatrix_Y;
0174 nZ = ge.hdr.image.slquant;     <span class="comment">% slice quantity (Nslices)</span>
0175 pX = ge.hdr.image.pixsize_X;
0176 pY = ge.hdr.image.pixsize_Y;
0177 pZ = ge.hdr.image.slthick + ge.hdr.image.scanspacing;
0178 
0179 [vX vY vZ] = size(ge.img);
0180 
0181 <span class="comment">% Reshape into axial radiological orientation (SPM compatible)</span>
0182 <span class="comment">% The default Analyze orientation is +X left, +Y anterior, +Z superior (LAS)</span>
0183 
0184 <span class="keyword">switch</span> orient,
0185     
0186 <span class="keyword">case</span>  0, <span class="comment">% Unknown Orientation</span>
0187     
0188     warning(<span class="string">'avw.img = ge.img without reorientation!\n'</span>);
0189     avw.img = ge.img;
0190     
0191 <span class="keyword">case</span> {1, -1}, <span class="comment">% Axial</span>
0192     avw.hdr.dime.dim(2:4)    = [ nX nY nZ ];
0193     avw.hdr.dime.pixdim(2:4) = [ pX pY pZ ];
0194     
0195     avw.img = ge.img;
0196     <span class="keyword">if</span> orient == 1, <span class="comment">% Axial (I to S)</span>
0197         <span class="comment">% checked this (03/2003), not sure of L/R orient</span>
0198         avw.img = flipdim(avw.img,2); <span class="comment">% flip to P to A</span>
0199     <span class="keyword">elseif</span> orient == -1, <span class="comment">% Axial (S to I)</span>
0200         <span class="comment">% have not checked this (03/2003)</span>
0201         avw.img = flipdim(avw.img,2); <span class="comment">% flip to P to A</span>
0202         avw.img = flipdim(avw.img,3); <span class="comment">% flip to I to S</span>
0203     <span class="keyword">end</span>
0204     
0205 <span class="keyword">case</span> {2, -2}, <span class="comment">% Sagittal</span>
0206     
0207     avw.hdr.dime.dim(2:4)    = [ nZ nX nY ];
0208     avw.hdr.dime.pixdim(2:4) = [ pZ pX pY ];
0209     
0210     avw.img = permute(ge.img,[3 1 2]);
0211     <span class="keyword">if</span> orient == 2, <span class="comment">% Sagittal (R to L)</span>
0212         <span class="comment">% have not checked this (03/2003)</span>
0213         avw.img = flipdim(avw.img,2); <span class="comment">% flip to P to A?</span>
0214         avw.img = flipdim(avw.img,3); <span class="comment">% flip to I to S?</span>
0215     <span class="keyword">elseif</span> orient == -2, <span class="comment">% Sagittal (L to R)</span>
0216         <span class="comment">% checked this (03/2003)</span>
0217         avw.img = flipdim(avw.img,1); <span class="comment">% flip to R to L</span>
0218         avw.img = flipdim(avw.img,2); <span class="comment">% flip to P to A</span>
0219         avw.img = flipdim(avw.img,3); <span class="comment">% flip to I to S</span>
0220     <span class="keyword">end</span>
0221     
0222 <span class="keyword">case</span> {3, -3}, <span class="comment">% Coronal</span>
0223     
0224     avw.hdr.dime.dim(2:4)    = [ nX nZ nY ];
0225     avw.hdr.dime.pixdim(2:4) = [ pX pZ pY ];
0226     
0227     avw.img = permute(ge.img,[1 3 2]);
0228     <span class="keyword">if</span> orient == 3, <span class="comment">% Coronal (P to A)</span>
0229         <span class="comment">% have not checked this (03/2003), not sure of L/R orient</span>
0230         avw.img = flipdim(avw.img,3); <span class="comment">% flip to I to S?</span>
0231     <span class="keyword">elseif</span> orient == -3, <span class="comment">% Coronal (A to P)</span>
0232         <span class="comment">% have not checked this (03/2003), not sure of L/R orient</span>
0233         avw.img = flipdim(avw.img,2); <span class="comment">% flip to P to A?</span>
0234         avw.img = flipdim(avw.img,3); <span class="comment">% flip to I to S?</span>
0235     <span class="keyword">end</span>
0236     
0237 <span class="keyword">end</span>
0238 
0239 <span class="comment">% Set the origin to the center of the volume (not sure this is valid, DLW)</span>
0240 <span class="comment">%avw.hdr.dime.originator = [floor(avw.hdr.dime.dim(2)/2) ...</span>
0241 <span class="comment">%                           floor(avw.hdr.dime.dim(3)/2) ...</span>
0242 <span class="comment">%                           floor(avw.hdr.dime.dim(4)/2) 0 0];</span>
0243 
0244 avw.hdr.dime.glmax = max(max(max(avw.img)));
0245 avw.hdr.hist.orient = <span class="string">'0'</span>;
0246 
0247 <span class="keyword">return</span></pre></div>
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