avw_img_read.m

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        n = n + PixelDim;
      end
    end
    
    % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim
    avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
    avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
    
    
    %--------------------------------------------------------------------------------
    % Orient values 3-5 have the second index reversed in order, essentially
    % 'flipping' the images relative to what would most likely become the vertical
    % axis of the displayed image.
    %--------------------------------------------------------------------------------
    
  case 3, % transverse/axial flipped
    
    % orient = 3:  The primary orientation of the data on disk is in the
    % transverse plane relative to the object scanned.  Most commonly, the fastest
    % moving index through the voxels that are part of this transverse image would
    % span the right-left extent of the structure imaged, with the next fastest
    % moving index spanning the *anterior-posterior* extent of the structure.  This
    % 'orient' flag would indicate to Analyze that this data should be placed in
    % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension
    % being the slice direction.
    
    % For the 'transverse flipped' type, the voxels are stored with
    % Pixels in 'x' axis (varies fastest) - from patient right to Left
    % Rows in   'y' axis                  - from patient anterior to Posterior *
    % Slices in 'z' axis                  - from patient inferior to Superior
    
    fprintf('...reading axial flipped (+Y from Anterior to Posterior)\n');
    
    avw.img = zeros(PixelDim,RowDim,SliceDim);
    
    n = 1;
    x = 1:PixelDim;
    for z = 1:SliceDim,
      for y = RowDim:-1:1, % flip in Y, read A2P file into P2A 3D matrix
        
        % load a flipped Y row of X values into Z slice avw.img
        avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
        n = n + PixelDim;
      end
    end
    
    % no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim
    
    
  case 4, % coronal flipped
    
    % orient = 4:  The primary orientation of the data on disk is in the coronal
    % plane relative to the object scanned.  Most commonly, the fastest moving
    % index through the voxels that are part of this coronal image would span the
    % right-left extent of the structure imaged, with the next fastest moving
    % index spanning the *superior-inferior* extent of the structure.  This 'orient'
    % flag would indicate to Analyze that this data should be placed in the X-Z
    % plane of the 3D Analyze Coordinate System, with the Y dimension being the
    % slice direction.
    
    % For the 'coronal flipped' type, the voxels are stored with
    % Pixels in 'x' axis (varies fastest) - from patient right to Left
    % Rows in   'z' axis                  - from patient superior to Inferior*
    % Slices in 'y' axis                  - from patient posterior to Anterior
    
    fprintf('...reading coronal flipped (+Z from Superior to Inferior)\n');
    
    avw.img = zeros(PixelDim,SliceDim,RowDim);
    
    n = 1;
    x = 1:PixelDim;
    for y = 1:SliceDim,
      for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix
        
        % load a flipped Z row of X values into Y slice avw.img
        avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
        n = n + PixelDim;
      end
    end
    
    % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim
    avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]);
    avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]);
    
    
  case 5, % sagittal flipped
    
    % orient = 5:  The primary orientation of the data on disk is in the sagittal
    % plane relative to the object scanned.  Most commonly, the fastest moving
    % index through the voxels that are part of this sagittal image would span the
    % posterior-anterior extent of the structure imaged, with the next fastest
    % moving index spanning the *superior-inferior* extent of the structure.  This
    % 'orient' flag would indicate to Analyze that this data should be placed in
    % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension
    % being the slice direction.
    
    % For the 'sagittal flipped' type, the voxels are stored with
    % Pixels in 'y' axis (varies fastest) - from patient posterior to Anterior
    % Rows in   'z' axis                  - from patient superior to Inferior*
    % Slices in 'x' axis                  - from patient right to Left
    
    fprintf('...reading sagittal flipped (+Z from Superior to Inferior)\n');
    
    avw.img = zeros(SliceDim,PixelDim,RowDim);
    
    n = 1;
    y = 1:PixelDim;
    
    for x = 1:SliceDim,
      for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix
        
        % load a flipped Z row of Y values into X slice avw.img
        avw.img(x,y,z) = tmp(n:n+(PixelDim-1));
        n = n + PixelDim;
      end
    end
    
    % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim
    avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]);
    avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]);
    
  otherwise
    
    error('unknown value in avw.hdr.hist.orient, try explicit IMGorient option.');
    
end

t=toc; fprintf('...done (%5.2f sec).\n\n',t);

return




% This function attempts to read the orientation of the
% Analyze file according to the hdr.hist.orient field of the 
% header.  Unfortunately, this field is optional and not
% all programs will set it correctly, so there is no guarantee,
% that the data loaded will be correctly oriented.  If necessary, 
% experiment with the 'orient' option to read the .img 
% data into the 3D matrix of avw.img as preferred.
% 

% (Conventions gathered from e-mail with [e-mail])
% 
% 0  transverse unflipped 
%       X direction first,  progressing from patient right to left, 
%       Y direction second, progressing from patient posterior to anterior, 
%       Z direction third,  progressing from patient inferior to superior. 
% 1  coronal unflipped 
%       X direction first,  progressing from patient right to left, 
%       Z direction second, progressing from patient inferior to superior, 
%       Y direction third,  progressing from patient posterior to anterior. 
% 2  sagittal unflipped 
%       Y direction first,  progressing from patient posterior to anterior, 
%       Z direction second, progressing from patient inferior to superior, 
%       X direction third,  progressing from patient right to left. 
% 3  transverse flipped 
%       X direction first,  progressing from patient right to left, 
%       Y direction second, progressing from patient anterior to posterior, 
%       Z direction third,  progressing from patient inferior to superior. 
% 4  coronal flipped 
%       X direction first,  progressing from patient right to left, 
%       Z direction second, progressing from patient superior to inferior, 
%       Y direction third,  progressing from patient posterior to anterior. 
% 5  sagittal flipped 
%       Y direction first,  progressing from patient posterior to anterior, 
%       Z direction second, progressing from patient superior to inferior, 
%       X direction third,  progressing from patient right to left. 


%----------------------------------------------------------------------------
% From ANALYZE documentation...
% 
% The ANALYZE coordinate system has an origin in the lower left 
% corner. That is, with the subject lying supine, the coordinate 
% origin is on the right side of the body (x), at the back (y), 
% and at the feet (z). This means that:
% 
% +X increases from right (R) to left (L)
% +Y increases from the back (posterior,P) to the front (anterior, A)
% +Z increases from the feet (inferior,I) to the head (superior, S)
% 
% The LAS orientation is the radiological convention, where patient 
% left is on the image right.  The alternative neurological
% convention is RAS (also Talairach convention).
% 
% A major advantage of the Analzye origin convention is that the 
% coordinate origin of each orthogonal orientation (transverse, 
% coronal, and sagittal) lies in the lower left corner of the 
% slice as it is displayed.
% 
% Orthogonal slices are numbered from one to the number of slices
% in that orientation. For example, a volume (x, y, z) dimensioned 
% 128, 256, 48 has: 
% 
%   128 sagittal   slices numbered 1 through 128 (X)
%   256 coronal    slices numbered 1 through 256 (Y)
%    48 transverse slices numbered 1 through  48 (Z)
% 
% Pixel coordinates are made with reference to the slice numbers from 
% which the pixels come. Thus, the first pixel in the volume is 
% referenced p(1,1,1) and not at p(0,0,0).
% 
% Transverse slices are in the XY plane (also known as axial slices).
% Sagittal slices are in the ZY plane. 
% Coronal slices are in the ZX plane. 
% 
%----------------------------------------------------------------------------


%----------------------------------------------------------------------------
% E-mail from [e-mail]
% 
% The 'orient' field in the data_history structure specifies the primary
% orientation of the data as it is stored in the file on disk.  This usually
% corresponds to the orientation in the plane of acquisition, given that this
% would correspond to the order in which the data is written to disk by the
% scanner or other software application.  As you know, this field will contain
% the values:
% 
% orient = 0 transverse unflipped
% 1 coronal unflipped
% 2 sagittal unflipped
% 3 transverse flipped
% 4 coronal flipped
% 5 sagittal flipped
% 
% It would be vary rare that you would ever encounter any old Analyze 7.5
% files that contain values of 'orient' which indicate that the data has been
% 'flipped'.  The 'flipped flag' values were really only used internal to
% Analyze to precondition data for fast display in the Movie module, where the
% images were actually flipped vertically in order to accommodate the raster
% paint order on older graphics devices.  The only cases you will encounter
% will have values of 0, 1, or 2.
% 
% As mentioned, the 'orient' flag only specifies the primary orientation of
% data as stored in the disk file itself.  It has nothing to do with the
% representation of the data in the 3D Analyze coordinate system, which always
% has a fixed representation to the data.  The meaning of the 'orient' values
% should be interpreted as follows:
% 
% orient = 0:  The primary orientation of the data on disk is in the
% transverse plane relative to the object scanned.  Most commonly, the fastest
% moving index through the voxels that are part of this transverse image would
% span the right-left extent of the structure imaged, with the next fastest
% moving index spanning the posterior-anterior extent of the structure.  This
% 'orient' flag would indicate to Analyze that this data should be placed in
% the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension
% being the slice direction.
% 
% orient = 1:  The primary orientation of the data on disk is in the coronal
% plane relative to the object scanned.  Most commonly, the fastest moving
% index through the voxels that are part of this coronal image would span the
% right-left extent of the structure imaged, with the next fastest moving
% index spanning the inferior-superior extent of the structure.  This 'orient'
% flag would indicate to Analyze that this data should be placed in the X-Z
% plane of the 3D Analyze Coordinate System, with the Y dimension being the
% slice direction.
% 
% orient = 2:  The primary orientation of the data on disk is in the sagittal
% plane relative to the object scanned.  Most commonly, the fastest moving
% index through the voxels that are part of this sagittal image would span the
% posterior-anterior extent of the structure imaged, with the next fastest
% moving index spanning the inferior-superior extent of the structure.  This
% 'orient' flag would indicate to Analyze that this data should be placed in
% the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension
% being the slice direction.
% 
% Orient values 3-5 have the second index reversed in order, essentially
% 'flipping' the images relative to what would most likely become the vertical
% axis of the displayed image.
% 
% Hopefully you understand the difference between the indication this 'orient'
% flag has relative to data stored on disk and the full 3D Analyze Coordinate
% System for data that is managed as a volume image.  As mentioned previously,
% the orientation of patient anatomy in the 3D Analyze Coordinate System has a
% fixed orientation relative to each of the orthogonal axes.  This orientation
% is completely described in the information that is attached, but the basics
% are:
% 
% Left-handed coordinate system
% 
% X-Y plane is Transverse
% X-Z plane is Coronal
% Y-Z plane is Sagittal
% 
% X axis runs from patient right (low X) to patient left (high X)
% Y axis runs from posterior (low Y) to anterior (high Y)
% Z axis runs from inferior (low Z) to superior (high Z)
% 
%----------------------------------------------------------------------------



%----------------------------------------------------------------------------
% SPM2 NOTES from spm2 webpage: One thing to watch out for is the image 
% orientation. The proper Analyze format uses a left-handed co-ordinate 
% system, whereas Talairach uses a right-handed one. In SPM99, images were 
% flipped at the spatial normalisation stage (from one co-ordinate system 
% to the other). In SPM2b, a different approach is used, so that either a 
% left- or right-handed co-ordinate system is used throughout. The SPM2b 
% program is told about the handedness that the images are stored with by 
% the spm_flip_analyze_images.m function and the defaults.analyze.flip 
% parameter that is specified in the spm_defaults.m file. These files are 
% intended to be customised for each site. If you previously used SPM99 
% and your images were flipped during spatial normalisation, then set 
% defaults.analyze.flip=1. If no flipping took place, then set 
% defaults.analyze.flip=0. Check that when using the Display facility
% (possibly after specifying some rigid-body rotations) that: 
% 
% The top-left image is coronal with the top (superior) of the head displayed 
% at the top and the left shown on the left. This is as if the subject is viewed 
% from behind. 
% 
% The bottom-left image is axial with the front (anterior) of the head at the 
% top and the left shown on the left. This is as if the subject is viewed from above. 
% 
% The top-right image is sagittal with the front (anterior) of the head at the 
% left and the top of the head shown at the top. This is as if the subject is 
% viewed from the left.
%----------------------------------------------------------------------------