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# avw_img_read

## (PublicToolbox/MRI_toolbox_v2p0/avw_img_read.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)

### Help Text

     avw_img_read - read Analyze format data image (*.img)

     [ avw, machine ] = avw_img_read(fileprefix, [orient], [machine])

     fileprefix - a string, the filename without the .img extension

     orient - read a specified orientation, integer values:

              '', use header history orient field
              0,  transverse unflipped (LAS*)
              1,  coronal unflipped (LA*S)
              2,  sagittal unflipped (L*AS)
              3,  transverse flipped (LPS*)
              4,  coronal flipped (LA*I)
              5,  sagittal flipped (L*AI)

     where * follows the slice dimension and letters indicate +XYZ
     orientations (L left, R right, A anterior, P posterior,
     I inferior, & S superior).

     Some files may contain data in the 3-5 orientations, but this
     is unlikely. For more information about orientation, see the
     documentation at the end of this .m file.  See also the
     AVW_FLIP function for orthogonal reorientation.

     machine - a string, see machineformat in fread for details.
               The default here is 'ieee-le' but the routine
               will automatically switch between little and big
               endian to read any such Analyze header.  It
               reports the appropriate machine format and can
               return the machine value.

     Returned values:

     avw.hdr - a struct with image data parameters.
     avw.img - a 3D matrix of image data (double precision).

     The returned 3D matrix will correspond with the
     default ANALYZE coordinate system, which
     is Left-handed:

     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)

     See also: avw_hdr_read (called by this function),
               avw_view, avw_write, avw_img_write, avw_flip

### Cross-Reference Information

This function calls

    avw_hdr_read                       C:\BrainStorm_2001\PublicToolbox\MRI_toolbox_v2p0\avw_hdr_read.m

This function is called by

    bst_mriviewer                      C:\BrainStorm_2001\Toolbox\bst_mriviewer.m

### Listing of function C:\BrainStorm_2001\PublicToolbox\MRI_toolbox_v2p0\avw_img_read.m

    function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)

    % avw_img_read - read Analyze format data image (*.img)
    %
    % [ avw, machine ] = avw_img_read(fileprefix, [orient], [machine])
    %
    % fileprefix - a string, the filename without the .img extension
    %
    % orient - read a specified orientation, integer values:
    %
    %          '', use header history orient field
    %          0,  transverse unflipped (LAS*)
    %          1,  coronal unflipped (LA*S)
    %          2,  sagittal unflipped (L*AS)
    %          3,  transverse flipped (LPS*)
    %          4,  coronal flipped (LA*I)
    %          5,  sagittal flipped (L*AI)
    %
    % where * follows the slice dimension and letters indicate +XYZ
    % orientations (L left, R right, A anterior, P posterior,
    % I inferior, & S superior).
    %
    % Some files may contain data in the 3-5 orientations, but this
    % is unlikely. For more information about orientation, see the
    % documentation at the end of this .m file.  See also the
    % AVW_FLIP function for orthogonal reorientation.
    %
    % machine - a string, see machineformat in fread for details.
    %           The default here is 'ieee-le' but the routine
    %           will automatically switch between little and big
    %           endian to read any such Analyze header.  It
    %           reports the appropriate machine format and can
    %           return the machine value.
    %
    % Returned values:
    %
    % avw.hdr - a struct with image data parameters.
    % avw.img - a 3D matrix of image data (double precision).
    %
    % The returned 3D matrix will correspond with the
    % default ANALYZE coordinate system, which
    % is Left-handed:
    %
    % 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)
    %
    % See also: avw_hdr_read (called by this function),
    %           avw_view, avw_write, avw_img_write, avw_flip
    %

    % $Revision: 1 $ $Date: 5/21/04 12:51p $

    % Licence:  GNU GPL, no express or implied warranties
    % History:  05/2002, Darren.Weber@flinders.edu.au
    %                    The Analyze format is copyright
    %                    (c) Copyright, 1986-1995
    %                    Biomedical Imaging Resource, Mayo Foundation
    %           01/2003, Darren.Weber@flinders.edu.au
    %                    - adapted for matlab v5
    %                    - revised all orientation information and handling
    %                      after seeking further advice from AnalyzeDirect.com
    %           03/2003, Darren.Weber@flinders.edu.au
    %                    - adapted for -ve pixdim values (non standard Analyze)
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    if ~exist('fileprefix','var'),
      msg = sprintf('...no input fileprefix - see help avw_img_read\n\n');
      error(msg);
    end
    if ~exist('IMGorient','var'), IMGorient = ''; end
    if ~exist('machine','var'), machine = 'ieee-le'; end

    if findstr('.hdr',fileprefix),
      fileprefix = strrep(fileprefix,'.hdr','');
    end
    if findstr('.img',fileprefix),
      fileprefix = strrep(fileprefix,'.img','');
    end

    % MAIN

    % Read the file header
    [ avw, machine ] = avw_hdr_read(fileprefix,machine);

    avw = read_image(avw,IMGorient,machine);

    return

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    function [ avw ] = read_image(avw,IMGorient,machine)

    fid = fopen(sprintf('%s.img',avw.fileprefix),'r',machine);
    if fid < 0,
      msg = sprintf('...cannot open file %s.img\n\n',avw.fileprefix);
      error(msg);
    end

    ver = '[$Revision: 1 $]';
    fprintf('\nAVW_IMG_READ [v%s]\n',ver(12:16));  tic;

    % short int bitpix;    /* Number of bits per pixel; 1, 8, 16, 32, or 64. */
    % short int datatype      /* Datatype for this image set */
    % /*Acceptable values for datatype are*/
    % #define DT_NONE             0
    % #define DT_UNKNOWN          0    /*Unknown data type*/
    % #define DT_BINARY           1    /*Binary             ( 1 bit per voxel)*/
    % #define DT_UNSIGNED_CHAR    2    /*Unsigned character ( 8 bits per voxel)*/
    % #define DT_SIGNED_SHORT     4    /*Signed short       (16 bits per voxel)*/
    % #define DT_SIGNED_INT       8    /*Signed integer     (32 bits per voxel)*/
    % #define DT_FLOAT           16    /*Floating point     (32 bits per voxel)*/
    % #define DT_COMPLEX         32    /*Complex (64 bits per voxel; 2 floating point numbers)/*
    % #define DT_DOUBLE          64    /*Double precision   (64 bits per voxel)*/
    % #define DT_RGB            128    /*A Red-Green-Blue datatype*/
    % #define DT_ALL            255    /*Undocumented*/

    switch double(avw.hdr.dime.bitpix),
      case  1,   precision = 'bit1';
      case  8,   precision = 'uchar';
      case 16,   precision = 'int16';
      case 32,
        if     isequal(avw.hdr.dime.datatype, 8), precision = 'int32';
        else                                      precision = 'single';
        end
      case 64,   precision = 'double';
      otherwise,
        precision = 'uchar';
        fprintf('...precision undefined in header, using ''uchar''\n');
    end

    % read the whole .img file into matlab (faster)
    fprintf('...reading %s Analyze %s image format.\n',machine,precision);
    fseek(fid,0,'bof');
    % adjust for matlab version
    ver = version;
    ver = str2num(ver(1));
    if ver < 6,
      tmp = fread(fid,inf,sprintf('%s',precision));
    else,
      tmp = fread(fid,inf,sprintf('%s=>double',precision));
    end
    fclose(fid);

    % Update the global min and max values
    avw.hdr.dime.glmax = max(double(tmp));
    avw.hdr.dime.glmin = min(double(tmp));

    %---------------------------------------------------------------
    % Now partition the img data into xyz

    % --- first figure out the size of the image

    % short int dim[ ];      /* Array of the image dimensions */
    %
    % dim[0]      Number of dimensions in database; usually 4.
    % dim[1]      Image X dimension;  number of pixels in an image row.
    % dim[2]      Image Y dimension;  number of pixel rows in slice.
    % dim[3]      Volume Z dimension; number of slices in a volume.
    % dim[4]      Time points; number of volumes in database.

    PixelDim = double(avw.hdr.dime.dim(2));
    RowDim   = double(avw.hdr.dime.dim(3));
    SliceDim = double(avw.hdr.dime.dim(4));

    PixelSz  = double(avw.hdr.dime.pixdim(2));
    RowSz    = double(avw.hdr.dime.pixdim(3));
    SliceSz  = double(avw.hdr.dime.pixdim(4));

    % ---- NON STANDARD ANALYZE...

    % Some Analyze files have been found to set -ve pixdim values, eg
    % the MNI template avg152T1_brain in the FSL etc/standard folder,
    % perhaps to indicate flipped orientation?  If so, this code below
    % will NOT handle the flip correctly!
    if PixelSz < 0,
      warning('X pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(2))');
      PixelSz = abs(PixelSz);
      avw.hdr.dime.pixdim(2) = single(PixelSz);
    end
    if RowSz < 0,
      warning('Y pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(3))');
      RowSz = abs(RowSz);
      avw.hdr.dime.pixdim(3) = single(RowSz);
    end
    if SliceSz < 0,
      warning('Z pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(4))');
      SliceSz = abs(SliceSz);
      avw.hdr.dime.pixdim(4) = single(SliceSz);
    end

    % ---- END OF NON STANDARD ANALYZE

    % --- check the orientation specification and arrange img accordingly
    if ~isempty(IMGorient),
      if ischar(IMGorient),
        avw.hdr.hist.orient = uint8(str2num(IMGorient));
      else
        avw.hdr.hist.orient = uint8(IMGorient);
      end
    end,

    if isempty(avw.hdr.hist.orient),
      msg = [ '...unspecified avw.hdr.hist.orient, using default 0\n',...
          '   (check image and try explicit IMGorient option).\n'];
      fprintf(msg);
      avw.hdr.hist.orient = uint8(0);
    end

    switch double(avw.hdr.hist.orient),

      case 0, % transverse unflipped

        % 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.

        % For the 'transverse unflipped' type, the voxels are stored with
        % Pixels in 'x' axis (varies fastest) - from patient right to left
        % Rows in   'y' axis                  - from patient posterior to anterior
        % Slices in 'z' axis                  - from patient inferior to superior

        fprintf('...reading axial unflipped orientation\n');

        avw.img = zeros(PixelDim,RowDim,SliceDim);

        n = 1;
        x = 1:PixelDim;
        for z = 1:SliceDim,
          for y = 1:RowDim,
            % load 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 1, % coronal unflipped

        % 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.

        % For the 'coronal unflipped' type, the voxels are stored with
        % Pixels in 'x' axis (varies fastest) - from patient right to left
        % Rows in   'z' axis                  - from patient inferior to superior
        % Slices in 'y' axis                  - from patient posterior to anterior

        fprintf('...reading coronal unflipped orientation\n');

        avw.img = zeros(PixelDim,SliceDim,RowDim);

        n = 1;
        x = 1:PixelDim;
        for y = 1:SliceDim,
          for z = 1:RowDim,
            % load 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 2, % sagittal unflipped

        % 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.

        % For the 'sagittal unflipped' type, the voxels are stored with
        % Pixels in 'y' axis (varies fastest) - from patient posterior to anterior
        % Rows in   'z' axis                  - from patient inferior to superior
        % Slices in 'x' axis                  - from patient right to left

        fprintf('...reading sagittal unflipped orientation\n');

        avw.img = zeros(SliceDim,PixelDim,RowDim);

        n = 1;
        y = 1:PixelDim;         % posterior to anterior (fastest)

        for x = 1:SliceDim,     % right to left (slowest)
          for z = 1:RowDim,   % inferior to superior

            % load 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]);

        %--------------------------------------------------------------------------------
        % 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 support@AnalyzeDirect.com)
    %
    % 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 support@AnalyzeDirect.com
    %
    % 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.
    %----------------------------------------------------------------------------

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