avw_hdr_read.m

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	%       int glmin;                       /* 104 + 4         */
	%       };                               /* total=108 bytes */
    
	dime.dim        = fread(fid,8,'*int16')';
	dime.vox_units  = fread(fid,4,'*char')';
	dime.cal_units  = fread(fid,8,'*char')';
	dime.unused1    = fread(fid,1,'*int16');
	dime.datatype   = fread(fid,1,'*int16');
	dime.bitpix     = fread(fid,1,'*int16');
	dime.dim_un0    = fread(fid,1,'*int16');
	dime.pixdim     = fread(fid,8,'*float')';
	dime.vox_offset = fread(fid,1,'*float');
	dime.roi_scale  = fread(fid,1,'*float');
	dime.funused1   = fread(fid,1,'*float');
	dime.funused2   = fread(fid,1,'*float');
	dime.cal_max    = fread(fid,1,'*float');
	dime.cal_min    = fread(fid,1,'*float');
	dime.compressed = fread(fid,1,'*int32');
	dime.verified   = fread(fid,1,'*int32');
	dime.glmax      = fread(fid,1,'*int32');
	dime.glmin      = fread(fid,1,'*int32');
	
    if dime.dim(1) < 4, % Number of dimensions in database; usually 4.
        fprintf('...ensuring 4 dimensions in avw.hdr.dime.dim\n');
        dime.dim(1) = int16(4);
    end
    if dime.dim(5) < 1, % Time points; number of volumes in database
        fprintf('...ensuring at least 1 volume in avw.hdr.dime.dim(5)\n');
        dime.dim(5) = int16(1);
    end
    
return

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [ hist ] = data_history(fid)
    
	% Original header structures - ANALYZE 7.5
	%struct data_history       
	%       {                                /* off + size      */
	%       char descrip[80];                /* 0 + 80          */
	%       char aux_file[24];               /* 80 + 24         */
	%       char orient;                     /* 104 + 1         */
	%       char originator[10];             /* 105 + 10        */
	%       char generated[10];              /* 115 + 10        */
	%       char scannum[10];                /* 125 + 10        */
	%       char patient_id[10];             /* 135 + 10        */
	%       char exp_date[10];               /* 145 + 10        */
	%       char exp_time[10];               /* 155 + 10        */
	%       char hist_un0[3];                /* 165 + 3         */
	%       int views                        /* 168 + 4         */
	%       int vols_added;                  /* 172 + 4         */
	%       int start_field;                 /* 176 + 4         */
	%       int field_skip;                  /* 180 + 4         */
	%       int omax;                        /* 184 + 4         */
	%       int omin;                        /* 188 + 4         */
	%       int smax;                        /* 192 + 4         */
	%       int smin;                        /* 196 + 4         */
	%       };                               /* total=200 bytes */
	
	hist.descrip     = fread(fid,80,'*char')';
	hist.aux_file    = fread(fid,24,'*char')';
	hist.orient      = fread(fid, 1,'*uint8');  % see note below on char
	hist.originator  = fread(fid,10,'*char')';
	hist.generated   = fread(fid,10,'*char')';
	hist.scannum     = fread(fid,10,'*char')';
	hist.patient_id  = fread(fid,10,'*char')';
	hist.exp_date    = fread(fid,10,'*char')';
	hist.exp_time    = fread(fid,10,'*char')';
	hist.hist_un0    = fread(fid, 3,'*char')';
	hist.views       = fread(fid, 1,'*int32');
	hist.vols_added  = fread(fid, 1,'*int32');
	hist.start_field = fread(fid, 1,'*int32');
	hist.field_skip  = fread(fid, 1,'*int32');
	hist.omax        = fread(fid, 1,'*int32');
	hist.omin        = fread(fid, 1,'*int32');
	hist.smax        = fread(fid, 1,'*int32');
	hist.smin        = fread(fid, 1,'*int32');
	
    % check if hist.orient was saved as ascii char value
    switch hist.orient,
        case 48, hist.orient = uint8(0);
        case 49, hist.orient = uint8(1);
        case 50, hist.orient = uint8(2);
        case 51, hist.orient = uint8(3);
        case 52, hist.orient = uint8(4);
        case 53, hist.orient = uint8(5);
    end
    
return


% Note on using char:
% The 'char orient' field in the header is intended to
% hold simply an 8-bit unsigned integer value, not the ASCII representation
% of the character for that value.  A single 'char' byte is often used to
% represent an integer value in Analyze if the known value range doesn't
% go beyond 0-255 - saves a byte over a short int, which may not mean
% much in today's computing environments, but given that this format
% has been around since the early 1980's, saving bytes here and there on
% older systems was important!  In this case, 'char' simply provides the
% byte of storage - not an indicator of the format for what is stored in
% this byte.  Generally speaking, anytime a single 'char' is used, it is
% probably meant to hold an 8-bit integer value, whereas if this has
% been dimensioned as an array, then it is intended to hold an ASCII
% character string, even if that was only a single character.
% Denny  <[e-mail]>


% Comments
% The header format is flexible and can be extended for new 
% user-defined data types. The essential structures of the header 
% are the header_key and the image_dimension.
%

% The required elements in the header_key substructure are: 
%
% int sizeof_header   Must indicate the byte size of the header file. 
% int extents         Should be 16384, the image file is created as 
%                     contiguous with a minimum extent size. 
% char regular        Must be 'r' to indicate that all images and 
%                     volumes are the same size. 
% 

% The image_dimension substructure describes the organization and 
% size of the images. These elements enable the database to reference 
% images by volume and slice number. Explanation of each element follows: 
% 
% 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.
% dim[5]      Undocumented.
% dim[6]      Undocumented.
% dim[7]      Undocumented.
% 
% char vox_units[4]     Specifies the spatial units of measure for a voxel. 
% char cal_units[8]      Specifies the name of the calibration unit. 
% short int unused1      /* Unused */ 
% 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*/
% 
% short int bitpix;    /* Number of bits per pixel; 1, 8, 16, 32, or 64. */ 
% short int dim_un0;   /* Unused */ 
% 
% float pixdim[];     Parallel array to dim[], giving real world measurements in mm and ms. 
%       pixdim[0];    Pixel dimensions? 
%       pixdim[1];    Voxel width in mm. 
%       pixdim[2];    Voxel height in mm. 
%       pixdim[3];    Slice thickness in mm. 
%       pixdim[4];    timeslice in ms (ie, TR in fMRI). 
%       pixdim[5];    Undocumented. 
%       pixdim[6];    Undocumented. 
%       pixdim[7];    Undocumented. 
% 
% float vox_offset;   Byte offset in the .img file at which voxels start. This value can be 
%                     negative to specify that the absolute value is applied for every image
%                     in the file. 
% 
% float roi_scale; Specifies the Region Of Interest scale? 
% float funused1; Undocumented. 
% float funused2; Undocumented. 
% 
% float cal_max; Specifies the upper bound of the range of calibration values. 
% float cal_min; Specifies the lower bound of the range of calibration values. 
% 
% int compressed; Undocumented. 
% int verified;   Undocumented. 
% 
% int glmax;    The maximum pixel value for the entire database. 
% int glmin;    The minimum pixel value for the entire database. 
% 
%