avw_img_read_4d.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.

0511     
0512 <span class="keyword">end</span>
0513 
0514 t=toc; fprintf(<span class="string">'...done (%5.2f sec).\n\n'</span>,t);
0515 
0516 <span class="keyword">return</span>
0517 
0518 
0519 
0520 
0521 <span class="comment">% This function attempts to read the orientation of the</span>
0522 <span class="comment">% Analyze file according to the hdr.hist.orient field of the</span>
0523 <span class="comment">% header.  Unfortunately, this field is optional and not</span>
0524 <span class="comment">% all programs will set it correctly, so there is no guarantee,</span>
0525 <span class="comment">% that the data loaded will be correctly oriented.  If necessary,</span>
0526 <span class="comment">% experiment with the 'orient' option to read the .img</span>
0527 <span class="comment">% data into the 3D matrix of avw.img as preferred.</span>
0528 <span class="comment">%</span>
0529 
0530 <span class="comment">% (Conventions gathered from e-mail with [e-mail])</span>
0531 <span class="comment">%</span>
0532 <span class="comment">% 0  transverse unflipped</span>
0533 <span class="comment">%       X direction first,  progressing from patient right to left,</span>
0534 <span class="comment">%       Y direction second, progressing from patient posterior to anterior,</span>
0535 <span class="comment">%       Z direction third,  progressing from patient inferior to superior.</span>
0536 <span class="comment">% 1  coronal unflipped</span>
0537 <span class="comment">%       X direction first,  progressing from patient right to left,</span>
0538 <span class="comment">%       Z direction second, progressing from patient inferior to superior,</span>
0539 <span class="comment">%       Y direction third,  progressing from patient posterior to anterior.</span>
0540 <span class="comment">% 2  sagittal unflipped</span>
0541 <span class="comment">%       Y direction first,  progressing from patient posterior to anterior,</span>
0542 <span class="comment">%       Z direction second, progressing from patient inferior to superior,</span>
0543 <span class="comment">%       X direction third,  progressing from patient right to left.</span>
0544 <span class="comment">% 3  transverse flipped</span>
0545 <span class="comment">%       X direction first,  progressing from patient right to left,</span>
0546 <span class="comment">%       Y direction second, progressing from patient anterior to posterior,</span>
0547 <span class="comment">%       Z direction third,  progressing from patient inferior to superior.</span>
0548 <span class="comment">% 4  coronal flipped</span>
0549 <span class="comment">%       X direction first,  progressing from patient right to left,</span>
0550 <span class="comment">%       Z direction second, progressing from patient superior to inferior,</span>
0551 <span class="comment">%       Y direction third,  progressing from patient posterior to anterior.</span>
0552 <span class="comment">% 5  sagittal flipped</span>
0553 <span class="comment">%       Y direction first,  progressing from patient posterior to anterior,</span>
0554 <span class="comment">%       Z direction second, progressing from patient superior to inferior,</span>
0555 <span class="comment">%       X direction third,  progressing from patient right to left.</span>
0556 
0557 
0558 <span class="comment">%----------------------------------------------------------------------------</span>
0559 <span class="comment">% From ANALYZE documentation...</span>
0560 <span class="comment">%</span>
0561 <span class="comment">% The ANALYZE coordinate system has an origin in the lower left</span>
0562 <span class="comment">% corner. That is, with the subject lying supine, the coordinate</span>
0563 <span class="comment">% origin is on the right side of the body (x), at the back (y),</span>
0564 <span class="comment">% and at the feet (z). This means that:</span>
0565 <span class="comment">%</span>
0566 <span class="comment">% +X increases from right (R) to left (L)</span>
0567 <span class="comment">% +Y increases from the back (posterior,P) to the front (anterior, A)</span>
0568 <span class="comment">% +Z increases from the feet (inferior,I) to the head (superior, S)</span>
0569 <span class="comment">%</span>
0570 <span class="comment">% The LAS orientation is the radiological convention, where patient</span>
0571 <span class="comment">% left is on the image right.  The alternative neurological</span>
0572 <span class="comment">% convention is RAS (also Talairach convention).</span>
0573 <span class="comment">%</span>
0574 <span class="comment">% A major advantage of the Analzye origin convention is that the</span>
0575 <span class="comment">% coordinate origin of each orthogonal orientation (transverse,</span>
0576 <span class="comment">% coronal, and sagittal) lies in the lower left corner of the</span>
0577 <span class="comment">% slice as it is displayed.</span>
0578 <span class="comment">%</span>
0579 <span class="comment">% Orthogonal slices are numbered from one to the number of slices</span>
0580 <span class="comment">% in that orientation. For example, a volume (x, y, z) dimensioned</span>
0581 <span class="comment">% 128, 256, 48 has:</span>
0582 <span class="comment">%</span>
0583 <span class="comment">%   128 sagittal   slices numbered 1 through 128 (X)</span>
0584 <span class="comment">%   256 coronal    slices numbered 1 through 256 (Y)</span>
0585 <span class="comment">%    48 transverse slices numbered 1 through  48 (Z)</span>
0586 <span class="comment">%</span>
0587 <span class="comment">% Pixel coordinates are made with reference to the slice numbers from</span>
0588 <span class="comment">% which the pixels come. Thus, the first pixel in the volume is</span>
0589 <span class="comment">% referenced p(1,1,1) and not at p(0,0,0).</span>
0590 <span class="comment">%</span>
0591 <span class="comment">% Transverse slices are in the XY plane (also known as axial slices).</span>
0592 <span class="comment">% Sagittal slices are in the ZY plane.</span>
0593 <span class="comment">% Coronal slices are in the ZX plane.</span>
0594 <span class="comment">%</span>
0595 <span class="comment">%----------------------------------------------------------------------------</span>
0596 
0597 
0598 <span class="comment">%----------------------------------------------------------------------------</span>
0599 <span class="comment">% E-mail from [e-mail]</span>
0600 <span class="comment">%</span>
0601 <span class="comment">% The 'orient' field in the data_history structure specifies the primary</span>
0602 <span class="comment">% orientation of the data as it is stored in the file on disk.  This usually</span>
0603 <span class="comment">% corresponds to the orientation in the plane of acquisition, given that this</span>
0604 <span class="comment">% would correspond to the order in which the data is written to disk by the</span>
0605 <span class="comment">% scanner or other software application.  As you know, this field will contain</span>
0606 <span class="comment">% the values:</span>
0607 <span class="comment">%</span>
0608 <span class="comment">% orient = 0 transverse unflipped</span>
0609 <span class="comment">% 1 coronal unflipped</span>
0610 <span class="comment">% 2 sagittal unflipped</span>
0611 <span class="comment">% 3 transverse flipped</span>
0612 <span class="comment">% 4 coronal flipped</span>
0613 <span class="comment">% 5 sagittal flipped</span>
0614 <span class="comment">%</span>
0615 <span class="comment">% It would be vary rare that you would ever encounter any old Analyze 7.5</span>
0616 <span class="comment">% files that contain values of 'orient' which indicate that the data has been</span>
0617 <span class="comment">% 'flipped'.  The 'flipped flag' values were really only used internal to</span>
0618 <span class="comment">% Analyze to precondition data for fast display in the Movie module, where the</span>
0619 <span class="comment">% images were actually flipped vertically in order to accommodate the raster</span>
0620 <span class="comment">% paint order on older graphics devices.  The only cases you will encounter</span>
0621 <span class="comment">% will have values of 0, 1, or 2.</span>
0622 <span class="comment">%</span>
0623 <span class="comment">% As mentioned, the 'orient' flag only specifies the primary orientation of</span>
0624 <span class="comment">% data as stored in the disk file itself.  It has nothing to do with the</span>
0625 <span class="comment">% representation of the data in the 3D Analyze coordinate system, which always</span>
0626 <span class="comment">% has a fixed representation to the data.  The meaning of the 'orient' values</span>
0627 <span class="comment">% should be interpreted as follows:</span>
0628 <span class="comment">%</span>
0629 <span class="comment">% orient = 0:  The primary orientation of the data on disk is in the</span>
0630 <span class="comment">% transverse plane relative to the object scanned.  Most commonly, the fastest</span>
0631 <span class="comment">% moving index through the voxels that are part of this transverse image would</span>
0632 <span class="comment">% span the right-left extent of the structure imaged, with the next fastest</span>
0633 <span class="comment">% moving index spanning the posterior-anterior extent of the structure.  This</span>
0634 <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0635 <span class="comment">% the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension</span>
0636 <span class="comment">% being the slice direction.</span>
0637 <span class="comment">%</span>
0638 <span class="comment">% orient = 1:  The primary orientation of the data on disk is in the coronal</span>
0639 <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0640 <span class="comment">% index through the voxels that are part of this coronal image would span the</span>
0641 <span class="comment">% right-left extent of the structure imaged, with the next fastest moving</span>
0642 <span class="comment">% index spanning the inferior-superior extent of the structure.  This 'orient'</span>
0643 <span class="comment">% flag would indicate to Analyze that this data should be placed in the X-Z</span>
0644 <span class="comment">% plane of the 3D Analyze Coordinate System, with the Y dimension being the</span>
0645 <span class="comment">% slice direction.</span>
0646 <span class="comment">%</span>
0647 <span class="comment">% orient = 2:  The primary orientation of the data on disk is in the sagittal</span>
0648 <span class="comment">% plane relative to the object scanned.  Most commonly, the fastest moving</span>
0649 <span class="comment">% index through the voxels that are part of this sagittal image would span the</span>
0650 <span class="comment">% posterior-anterior extent of the structure imaged, with the next fastest</span>
0651 <span class="comment">% moving index spanning the inferior-superior extent of the structure.  This</span>
0652 <span class="comment">% 'orient' flag would indicate to Analyze that this data should be placed in</span>
0653 <span class="comment">% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension</span>
0654 <span class="comment">% being the slice direction.</span>
0655 <span class="comment">%</span>
0656 <span class="comment">% Orient values 3-5 have the second index reversed in order, essentially</span>
0657 <span class="comment">% 'flipping' the images relative to what would most likely become the vertical</span>
0658 <span class="comment">% axis of the displayed image.</span>
0659 <span class="comment">%</span>
0660 <span class="comment">% Hopefully you understand the difference between the indication this 'orient'</span>
0661 <span class="comment">% flag has relative to data stored on disk and the full 3D Analyze Coordinate</span>
0662 <span class="comment">% System for data that is managed as a volume image.  As mentioned previously,</span>
0663 <span class="comment">% the orientation of patient anatomy in the 3D Analyze Coordinate System has a</span>
0664 <span class="comment">% fixed orientation relative to each of the orthogonal axes.  This orientation</span>
0665 <span class="comment">% is completely described in the information that is attached, but the basics</span>
0666 <span class="comment">% are:</span>
0667 <span class="comment">%</span>
0668 <span class="comment">% Left-handed coordinate system</span>
0669 <span class="comment">%</span>
0670 <span class="comment">% X-Y plane is Transverse</span>
0671 <span class="comment">% X-Z plane is Coronal</span>
0672 <span class="comment">% Y-Z plane is Sagittal</span>
0673 <span class="comment">%</span>
0674 <span class="comment">% X axis runs from patient right (low X) to patient left (high X)</span>
0675 <span class="comment">% Y axis runs from posterior (low Y) to anterior (high Y)</span>
0676 <span class="comment">% Z axis runs from inferior (low Z) to superior (high Z)</span>
0677 <span class="comment">%</span>
0678 <span class="comment">%----------------------------------------------------------------------------</span>
0679 
0680 
0681 
0682 <span class="comment">%----------------------------------------------------------------------------</span>
0683 <span class="comment">% SPM2 NOTES from spm2 webpage: One thing to watch out for is the image</span>
0684 <span class="comment">% orientation. The proper Analyze format uses a left-handed co-ordinate</span>
0685 <span class="comment">% system, whereas Talairach uses a right-handed one. In SPM99, images were</span>
0686 <span class="comment">% flipped at the spatial normalisation stage (from one co-ordinate system</span>
0687 <span class="comment">% to the other). In SPM2b, a different approach is used, so that either a</span>
0688 <span class="comment">% left- or right-handed co-ordinate system is used throughout. The SPM2b</span>
0689 <span class="comment">% program is told about the handedness that the images are stored with by</span>
0690 <span class="comment">% the spm_flip_analyze_images.m function and the defaults.analyze.flip</span>
0691 <span class="comment">% parameter that is specified in the spm_defaults.m file. These files are</span>
0692 <span class="comment">% intended to be customised for each site. If you previously used SPM99</span>
0693 <span class="comment">% and your images were flipped during spatial normalisation, then set</span>
0694 <span class="comment">% defaults.analyze.flip=1. If no flipping took place, then set</span>
0695 <span class="comment">% defaults.analyze.flip=0. Check that when using the Display facility</span>
0696 <span class="comment">% (possibly after specifying some rigid-body rotations) that:</span>
0697 <span class="comment">%</span>
0698 <span class="comment">% The top-left image is coronal with the top (superior) of the head displayed</span>
0699 <span class="comment">% at the top and the left shown on the left. This is as if the subject is viewed</span>
0700 <span class="comment">% from behind.</span>
0701 <span class="comment">%</span>
0702 <span class="comment">% The bottom-left image is axial with the front (anterior) of the head at the</span>
0703 <span class="comment">% top and the left shown on the left. This is as if the subject is viewed from above.</span>
0704 <span class="comment">%</span>
0705 <span class="comment">% The top-right image is sagittal with the front (anterior) of the head at the</span>
0706 <span class="comment">% left and the top of the head shown at the top. This is as if the subject is</span>
0707 <span class="comment">% viewed from the left.</span>
0708 <span class="comment">%----------------------------------------------------------------------------</span></pre></div>
<hr><address>Generated on Fri 21-May-2004 12:38:21 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/">m2html</a></strong> &copy; 2003</address>
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