avw_img_read_4d.html

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0308     
0309     avw.img = zeros(PixelDim,RowDim,SliceDim);
0310     
0311     n = 1;
0312     x = 1:PixelDim;
0313     <span class="keyword">for</span> z = 1:SliceDim,
0314       <span class="keyword">for</span> y = 1:RowDim,
0315         <span class="comment">% load Y row of X values into Z slice avw.img</span>
0316         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0317         n = n + PixelDim;
0318       <span class="keyword">end</span>
0319     <span class="keyword">end</span>
0320     
0321     <span class="comment">% no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0322     
0323     
0324   <span class="keyword">case</span> 1, <span class="comment">% coronal unflipped</span>
0325     
0326     <span class="comment">% orient = 1:  The primary orientation of the data on disk is in the coronal</span>
0327     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0328     <span class="comment">% index through the voxels that are part of this coronal image would span the</span>
0329     <span class="comment">% right-&gt;left extent of the structure imaged, with the next fastest moving</span>
0330     <span class="comment">% index spanning the inferior-&gt;superior extent of the structure.  This 'orient'</span>
0331     <span class="comment">% flag would indicate to Analyze that this data should be placed in the X-Z</span>
0332     <span class="comment">% plane of the 3D Analyze Coordinate System, with the Y dimension being the</span>
0333     <span class="comment">% slice direction.</span>
0334     
0335     <span class="comment">% For the 'coronal unflipped' type, the voxels are stored with</span>
0336     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to left</span>
0337     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0338     <span class="comment">% Slices in 'y' axis                  - from patient posterior to anterior</span>
0339     
0340     fprintf(<span class="string">'...reading coronal unflipped orientation\n'</span>);
0341     
0342     avw.img = zeros(PixelDim,SliceDim,RowDim);
0343     
0344     n = 1;
0345     x = 1:PixelDim;
0346     <span class="keyword">for</span> y = 1:SliceDim,
0347       <span class="keyword">for</span> z = 1:RowDim,
0348         <span class="comment">% load Z row of X values into Y slice avw.img</span>
0349         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0350         n = n + PixelDim;
0351       <span class="keyword">end</span>
0352     <span class="keyword">end</span>
0353     
0354     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0355     avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]);
0356     avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]);
0357     
0358     
0359   <span class="keyword">case</span> 2, <span class="comment">% sagittal unflipped</span>
0360     
0361     <span class="comment">% orient = 2:  The primary orientation of the data on disk is in the sagittal</span>
0362     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0363     <span class="comment">% index through the voxels that are part of this sagittal image would span the</span>
0364     <span class="comment">% posterior-&gt;anterior extent of the structure imaged, with the next fastest</span>
0365     <span class="comment">% moving index spanning the inferior-&gt;superior extent of the structure.  This</span>
0366     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0367     <span class="comment">% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension</span>
0368     <span class="comment">% being the slice direction.</span>
0369     
0370     <span class="comment">% For the 'sagittal unflipped' type, the voxels are stored with</span>
0371     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to anterior</span>
0372     <span class="comment">% Rows in   'z' axis                  - from patient inferior to superior</span>
0373     <span class="comment">% Slices in 'x' axis                  - from patient right to left</span>
0374     
0375     fprintf(<span class="string">'...reading sagittal unflipped orientation\n'</span>);
0376     
0377     avw.img = zeros(SliceDim,PixelDim,RowDim);
0378     
0379     n = 1;
0380     y = 1:PixelDim;         <span class="comment">% posterior to anterior (fastest)</span>
0381     
0382     <span class="keyword">for</span> x = 1:SliceDim,     <span class="comment">% right to left (slowest)</span>
0383       <span class="keyword">for</span> z = 1:RowDim,   <span class="comment">% inferior to superior</span>
0384         
0385         <span class="comment">% load Z row of Y values into X slice avw.img</span>
0386         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0387         n = n + PixelDim;
0388       <span class="keyword">end</span>
0389     <span class="keyword">end</span>
0390     
0391     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0392     avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
0393     avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
0394     
0395     
0396     <span class="comment">%--------------------------------------------------------------------------------</span>
0397     <span class="comment">% Orient values 3-5 have the second index reversed in order, essentially</span>
0398     <span class="comment">% 'flipping' the images relative to what would most likely become the vertical</span>
0399     <span class="comment">% axis of the displayed image.</span>
0400     <span class="comment">%--------------------------------------------------------------------------------</span>
0401     
0402   <span class="keyword">case</span> 3, <span class="comment">% transverse/axial flipped</span>
0403     
0404     <span class="comment">% orient = 3:  The primary orientation of the data on disk is in the</span>
0405     <span class="comment">% transverse plane relative to the object scanned.  Most commonly, the fastest</span>
0406     <span class="comment">% moving index through the voxels that are part of this transverse image would</span>
0407     <span class="comment">% span the right-&gt;left extent of the structure imaged, with the next fastest</span>
0408     <span class="comment">% moving index spanning the *anterior-&gt;posterior* extent of the structure.  This</span>
0409     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0410     <span class="comment">% the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension</span>
0411     <span class="comment">% being the slice direction.</span>
0412     
0413     <span class="comment">% For the 'transverse flipped' type, the voxels are stored with</span>
0414     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to Left</span>
0415     <span class="comment">% Rows in   'y' axis                  - from patient anterior to Posterior *</span>
0416     <span class="comment">% Slices in 'z' axis                  - from patient inferior to Superior</span>
0417     
0418     fprintf(<span class="string">'...reading axial flipped (+Y from Anterior to Posterior)\n'</span>);
0419     
0420     avw.img = zeros(PixelDim,RowDim,SliceDim);
0421     
0422     n = 1;
0423     x = 1:PixelDim;
0424     <span class="keyword">for</span> z = 1:SliceDim,
0425       <span class="keyword">for</span> y = RowDim:-1:1, <span class="comment">% flip in Y, read A2P file into P2A 3D matrix</span>
0426         
0427         <span class="comment">% load a flipped Y row of X values into Z slice avw.img</span>
0428         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0429         n = n + PixelDim;
0430       <span class="keyword">end</span>
0431     <span class="keyword">end</span>
0432     
0433     <span class="comment">% no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0434     
0435     
0436   <span class="keyword">case</span> 4, <span class="comment">% coronal flipped</span>
0437     
0438     <span class="comment">% orient = 4:  The primary orientation of the data on disk is in the coronal</span>
0439     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0440     <span class="comment">% index through the voxels that are part of this coronal image would span the</span>
0441     <span class="comment">% right-&gt;left extent of the structure imaged, with the next fastest moving</span>
0442     <span class="comment">% index spanning the *superior-&gt;inferior* extent of the structure.  This 'orient'</span>
0443     <span class="comment">% flag would indicate to Analyze that this data should be placed in the X-Z</span>
0444     <span class="comment">% plane of the 3D Analyze Coordinate System, with the Y dimension being the</span>
0445     <span class="comment">% slice direction.</span>
0446     
0447     <span class="comment">% For the 'coronal flipped' type, the voxels are stored with</span>
0448     <span class="comment">% Pixels in 'x' axis (varies fastest) - from patient right to Left</span>
0449     <span class="comment">% Rows in   'z' axis                  - from patient superior to Inferior*</span>
0450     <span class="comment">% Slices in 'y' axis                  - from patient posterior to Anterior</span>
0451     
0452     fprintf(<span class="string">'...reading coronal flipped (+Z from Superior to Inferior)\n'</span>);
0453     
0454     avw.img = zeros(PixelDim,SliceDim,RowDim);
0455     
0456     n = 1;
0457     x = 1:PixelDim;
0458     <span class="keyword">for</span> y = 1:SliceDim,
0459       <span class="keyword">for</span> z = RowDim:-1:1, <span class="comment">% flip in Z, read S2I file into I2S 3D matrix</span>
0460         
0461         <span class="comment">% load a flipped Z row of X values into Y slice avw.img</span>
0462         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0463         n = n + PixelDim;
0464       <span class="keyword">end</span>
0465     <span class="keyword">end</span>
0466     
0467     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0468     avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]);
0469     avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]);
0470     
0471     
0472   <span class="keyword">case</span> 5, <span class="comment">% sagittal flipped</span>
0473     
0474     <span class="comment">% orient = 5:  The primary orientation of the data on disk is in the sagittal</span>
0475     <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0476     <span class="comment">% index through the voxels that are part of this sagittal image would span the</span>
0477     <span class="comment">% posterior-&gt;anterior extent of the structure imaged, with the next fastest</span>
0478     <span class="comment">% moving index spanning the *superior-&gt;inferior* extent of the structure.  This</span>
0479     <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0480     <span class="comment">% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension</span>
0481     <span class="comment">% being the slice direction.</span>
0482     
0483     <span class="comment">% For the 'sagittal flipped' type, the voxels are stored with</span>
0484     <span class="comment">% Pixels in 'y' axis (varies fastest) - from patient posterior to Anterior</span>
0485     <span class="comment">% Rows in   'z' axis                  - from patient superior to Inferior*</span>
0486     <span class="comment">% Slices in 'x' axis                  - from patient right to Left</span>
0487     
0488     fprintf(<span class="string">'...reading sagittal flipped (+Z from Superior to Inferior)\n'</span>);
0489     
0490     avw.img = zeros(SliceDim,PixelDim,RowDim);
0491     
0492     n = 1;
0493     y = 1:PixelDim;
0494     
0495     <span class="keyword">for</span> x = 1:SliceDim,
0496       <span class="keyword">for</span> z = RowDim:-1:1, <span class="comment">% flip in Z, read S2I file into I2S 3D matrix</span>
0497         
0498         <span class="comment">% load a flipped Z row of Y values into X slice avw.img</span>
0499         avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
0500         n = n + PixelDim;
0501       <span class="keyword">end</span>
0502     <span class="keyword">end</span>
0503     
0504     <span class="comment">% rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim</span>
0505     avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
0506     avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
0507     
0508   <span class="keyword">otherwise</span>
0509     
0510     error(<span class="string">'unknown value in avw.hdr.hist.orient, try explicit IMGorient option.'</span>);