avw_img_read.html

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0278     
0279     avw.img = zeros(PixelDim,SliceDim,RowDim);
0280     
0281     n = 1;
0282     x = 1:PixelDim;
0283     <span class="keyword">for</span> y = 1:SliceDim,
0284       <span class="keyword">for</span> z = 1:RowDim,
0285         <span class="comment">% load Z row of X values into Y slice avw.img</span>
0286         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0287         n = n + PixelDim;
0288       <span class="keyword">end</span>
0289     <span class="keyword">end</span>
0290     
0291     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0292     avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]);
0293     avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]);
0294     
0295     
0296   <span class="keyword">case</span> 2, <span class="comment">% sagittal unflipped</span>
0297     
0298     <span class="comment">% orient = 2:  The primary orientation of the data on disk is in the sagittal</span>
0299     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0300     <span class="comment">% index through the voxels that are part of this sagittal image would span the</span>
0301     <span class="comment">% posterior-anterior extent of the structure imaged, with the next fastest</span>
0302     <span class="comment">% moving index spanning the inferior-superior extent of the structure.  This</span>
0303     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0304     <span class="comment">% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension</span>
0305     <span class="comment">% being the slice direction.</span>
0306     
0307     <span class="comment">% For the 'sagittal unflipped' type, the voxels are stored with</span>
0308     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to anterior</span>
0309     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0310     <span class="comment">% Slices in 'x' axis                  - from patient right to left</span>
0311     
0312     fprintf(<span class="string">'...reading sagittal unflipped orientation\n'</span>);
0313     
0314     avw.img = zeros(SliceDim,PixelDim,RowDim);
0315     
0316     n = 1;
0317     y = 1:PixelDim;         <span class="comment">% posterior to anterior (fastest)</span>
0318     
0319     <span class="keyword">for</span> x = 1:SliceDim,     <span class="comment">% right to left (slowest)</span>
0320       <span class="keyword">for</span> z = 1:RowDim,   <span class="comment">% inferior to superior</span>
0321         
0322         <span class="comment">% load Z row of Y values into X slice avw.img</span>
0323         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0324         n = n + PixelDim;
0325       <span class="keyword">end</span>
0326     <span class="keyword">end</span>
0327     
0328     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0329     avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
0330     avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
0331     
0332     
0333     <span class="comment">%--------------------------------------------------------------------------------</span>
0334     <span class="comment">% Orient values 3-5 have the second index reversed in order, essentially</span>
0335     <span class="comment">% 'flipping' the images relative to what would most likely become the vertical</span>
0336     <span class="comment">% axis of the displayed image.</span>
0337     <span class="comment">%--------------------------------------------------------------------------------</span>
0338     
0339   <span class="keyword">case</span> 3, <span class="comment">% transverse/axial flipped</span>
0340     
0341     <span class="comment">% orient = 3:  The primary orientation of the data on disk is in the</span>
0342     <span class="comment">% transverse plane relative to the object scanned.  Most commonly, the fastest</span>
0343     <span class="comment">% moving index through the voxels that are part of this transverse image would</span>
0344     <span class="comment">% span the right-left extent of the structure imaged, with the next fastest</span>
0345     <span class="comment">% moving index spanning the *anterior-posterior* extent of the structure.  This</span>
0346     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0347     <span class="comment">% the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension</span>
0348     <span class="comment">% being the slice direction.</span>
0349     
0350     <span class="comment">% For the 'transverse flipped' type, the voxels are stored with</span>
0351     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to Left</span>
0352     <span class="comment">% Rows in   'y' axis                  - from patient anterior to Posterior *</span>
0353     <span class="comment">% Slices in 'z' axis                  - from patient inferior to Superior</span>
0354     
0355     fprintf(<span class="string">'...reading axial flipped (+Y from Anterior to Posterior)\n'</span>);
0356     
0357     avw.img = zeros(PixelDim,RowDim,SliceDim);
0358     
0359     n = 1;
0360     x = 1:PixelDim;
0361     <span class="keyword">for</span> z = 1:SliceDim,
0362       <span class="keyword">for</span> y = RowDim:-1:1, <span class="comment">% flip in Y, read A2P file into P2A 3D matrix</span>
0363         
0364         <span class="comment">% load a flipped Y row of X values into Z slice avw.img</span>
0365         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0366         n = n + PixelDim;
0367       <span class="keyword">end</span>
0368     <span class="keyword">end</span>
0369     
0370     <span class="comment">% no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0371     
0372     
0373   <span class="keyword">case</span> 4, <span class="comment">% coronal flipped</span>
0374     
0375     <span class="comment">% orient = 4:  The primary orientation of the data on disk is in the coronal</span>
0376     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0377     <span class="comment">% index through the voxels that are part of this coronal image would span the</span>
0378     <span class="comment">% right-left extent of the structure imaged, with the next fastest moving</span>
0379     <span class="comment">% index spanning the *superior-inferior* extent of the structure.  This 'orient'</span>
0380     <span class="comment">% flag would indicate to Analyze that this data should be placed in the X-Z</span>
0381     <span class="comment">% plane of the 3D Analyze Coordinate System, with the Y dimension being the</span>
0382     <span class="comment">% slice direction.</span>
0383     
0384     <span class="comment">% For the 'coronal flipped' type, the voxels are stored with</span>
0385     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to Left</span>
0386     <span class="comment">% Rows in   'z' axis                  - from patient superior to Inferior*</span>
0387     <span class="comment">% Slices in 'y' axis                  - from patient posterior to Anterior</span>
0388     
0389     fprintf(<span class="string">'...reading coronal flipped (+Z from Superior to Inferior)\n'</span>);
0390     
0391     avw.img = zeros(PixelDim,SliceDim,RowDim);
0392     
0393     n = 1;
0394     x = 1:PixelDim;
0395     <span class="keyword">for</span> y = 1:SliceDim,
0396       <span class="keyword">for</span> z = RowDim:-1:1, <span class="comment">% flip in Z, read S2I file into I2S 3D matrix</span>
0397         
0398         <span class="comment">% load a flipped Z row of X values into Y slice avw.img</span>
0399         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0400         n = n + PixelDim;
0401       <span class="keyword">end</span>
0402     <span class="keyword">end</span>
0403     
0404     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0405     avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]);
0406     avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]);
0407     
0408     
0409   <span class="keyword">case</span> 5, <span class="comment">% sagittal flipped</span>
0410     
0411     <span class="comment">% orient = 5:  The primary orientation of the data on disk is in the sagittal</span>
0412     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0413     <span class="comment">% index through the voxels that are part of this sagittal image would span the</span>
0414     <span class="comment">% posterior-anterior extent of the structure imaged, with the next fastest</span>
0415     <span class="comment">% moving index spanning the *superior-inferior* extent of the structure.  This</span>
0416     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0417     <span class="comment">% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension</span>
0418     <span class="comment">% being the slice direction.</span>
0419     
0420     <span class="comment">% For the 'sagittal flipped' type, the voxels are stored with</span>
0421     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to Anterior</span>
0422     <span class="comment">% Rows in   'z' axis                  - from patient superior to Inferior*</span>
0423     <span class="comment">% Slices in 'x' axis                  - from patient right to Left</span>
0424     
0425     fprintf(<span class="string">'...reading sagittal flipped (+Z from Superior to Inferior)\n'</span>);
0426     
0427     avw.img = zeros(SliceDim,PixelDim,RowDim);
0428     
0429     n = 1;
0430     y = 1:PixelDim;
0431     
0432     <span class="keyword">for</span> x = 1:SliceDim,
0433       <span class="keyword">for</span> z = RowDim:-1:1, <span class="comment">% flip in Z, read S2I file into I2S 3D matrix</span>
0434         
0435         <span class="comment">% load a flipped Z row of Y values into X slice avw.img</span>
0436         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0437         n = n + PixelDim;
0438       <span class="keyword">end</span>
0439     <span class="keyword">end</span>
0440     
0441     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0442     avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
0443     avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
0444     
0445   <span class="keyword">otherwise</span>
0446     
0447     error(<span class="string">'unknown value in avw.hdr.hist.orient, try explicit IMGorient option.'</span>);
0448     
0449 <span class="keyword">end</span>
0450 
0451 t=toc; fprintf(<span class="string">'...done (%5.2f sec).\n\n'</span>,t);
0452 
0453 <span class="keyword">return</span>
0454 
0455 
0456 
0457 
0458 <span class="comment">% This function attempts to read the orientation of the</span>
0459 <span class="comment">% Analyze file according to the hdr.hist.orient field of the</span>
0460 <span class="comment">% header.  Unfortunately, this field is optional and not</span>
0461 <span class="comment">% all programs will set it correctly, so there is no guarantee,</span>
0462 <span class="comment">% that the data loaded will be correctly oriented.  If necessary,</span>
0463 <span class="comment">% experiment with the 'orient' option to read the .img</span>