Description of spm

0001 function [DIM,VOX,SCALE,TYPE,OFFSET,ORIGIN,DESCRIP] = spm_hread(P)
0002 % reads a header
0003 % FORMAT [DIM VOX SCALE TYPE OFFSET ORIGIN DESCRIP] = spm_hread(P);
0004 %
0005 % P       - filename          (e.g spm or spm.img)
0006 % DIM     - image size       [i j k [l]] (voxels)
0007 % VOX     - voxel size       [x y z [t]] (mm [secs])
0008 % SCALE   - scale factor
0009 % TYPE    - datatype (integer - see spm_type)
0010 % OFFSET  - offset (bytes)
0011 % ORIGIN  - origin [i j k]
0012 % DESCRIP - description string
0013 %___________________________________________________________________________
0014 %
0015 % spm_hread reads variables into working memory from a SPM/ANALYZE
0016 % compatible header file.  If the header does not exist global defaults
0017 % are used.  The 'originator' field of the ANALYZE format has been
0018 % changed to ORIGIN in the SPM version of the header.  funused1 of the
0019 % ANALYZE format is used for SCALE
0020 %
0021 % see also dbh.h (ANALYZE) spm_hwrite.m and spm_type.m
0022 %
0023 %__________________________________________________________________________
0024 % @(#)spm_hread.m    2.7 99/10/29
0025 
0026 % ensure correct suffix {.hdr}
0027 %---------------------------------------------------------------------------
0028 P     = deblank(P);
0029 q     = length(P);
0030 if q>=4 & P(q - 3) == '.'; P = P(1:(q - 4)); end
0031 P     = [P '.hdr'];
0032 
0033 % open header file
0034 %---------------------------------------------------------------------------
0035 fid   = fopen(P,'r','ieee-le');
0036 
0037 if (fid > 0)
0038 
0039 % read (struct) header_key
0040 %---------------------------------------------------------------------------
0041 fseek(fid,0,'bof');
0042 
0043 otherendian = 0;
0044 sizeof_hdr     = fread(fid,1,'*int32');
0045 
0046 % size of header must be 348 bytes
0047 if ~isequal(sizeof_hdr,348),
0048     % Re-open other-endian
0049     fclose(fid);
0050     fid = fopen(P,'r','ieee-be');
0051     fseek(fid,0,'bof');
0052     sizeof_hdr = fread(fid,1,'*int32');
0053     otherendian = 1;
0054 end;
0055 
0056 if ~isequal(sizeof_hdr,348),
0057     % Now throw an error
0058     msg = '...size of header not equal to 348 bytes!\n\n';
0059     error(msg);
0060 end
0061 
0062 data_type      = mysetstr(fread(fid,10,'uchar'))';
0063 db_name        = mysetstr(fread(fid,18,'uchar'))';
0064 extents        = fread(fid,1,'int32');
0065 session_error   = fread(fid,1,'int16');
0066 regular        = mysetstr(fread(fid,1,'uchar'))';
0067 hkey_un0        = mysetstr(fread(fid,1,'uchar'))';
0068 
0069 
0070 
0071 % read (struct) image_dimension
0072 %---------------------------------------------------------------------------
0073 fseek(fid,40,'bof');
0074 
0075 dim            = fread(fid,8,'int16');
0076 vox_units        = mysetstr(fread(fid,4,'uchar'))';
0077 cal_units        = mysetstr(fread(fid,8,'uchar'))';
0078 unused1        = fread(fid,1,'int16');
0079 datatype    = fread(fid,1,'int16');
0080 bitpix        = fread(fid,1,'int16');
0081 dim_un0        = fread(fid,1,'int16');
0082 pixdim        = fread(fid,8,'float');
0083 vox_offset    = fread(fid,1,'float');
0084 funused1    = fread(fid,1,'float');
0085 funused2    = fread(fid,1,'float');
0086 funused3    = fread(fid,1,'float');
0087 cal_max        = fread(fid,1,'float');
0088 cal_min        = fread(fid,1,'float');
0089 compressed    = fread(fid,1,'int32');
0090 verified    = fread(fid,1,'int32');
0091 glmax        = fread(fid,1,'int32');
0092 glmin        = fread(fid,1,'int32');
0093 
0094 % read (struct) data_history
0095 %---------------------------------------------------------------------------
0096 fseek(fid,148,'bof');
0097 
0098 descrip        = mysetstr(fread(fid,80,'uchar'))';
0099 aux_file    = mysetstr(fread(fid,24,'uchar'))';
0100 orient        = fread(fid,1,'uchar');
0101 origin        = fread(fid,5,'int16');
0102 generated    = mysetstr(fread(fid,10,'uchar'))';
0103 scannum        = mysetstr(fread(fid,10,'uchar'))';
0104 patient_id    = mysetstr(fread(fid,10,'uchar'))';
0105 exp_date    = mysetstr(fread(fid,10,'uchar'))';
0106 exp_time    = mysetstr(fread(fid,10,'uchar'))';
0107 hist_un0    = mysetstr(fread(fid,3,'uchar'))';
0108 views        = fread(fid,1,'int32');
0109 vols_added    = fread(fid,1,'int32');
0110 start_field    = fread(fid,1,'int32');
0111 field_skip    = fread(fid,1,'int32');
0112 omax        = fread(fid,1,'int32');
0113 omin        = fread(fid,1,'int32');
0114 smax        = fread(fid,1,'int32');
0115 smin        = fread(fid,1,'int32');
0116 
0117 fclose(fid);
0118 
0119 if isempty(smin)
0120     error(['There is a problem with the header file ' P '.']);
0121 end
0122 
0123 % convert to SPM global variables
0124 %---------------------------------------------------------------------------
0125 DIM              = dim(2:4)';
0126 VOX           = pixdim(2:4)';
0127 SCALE         = funused1;
0128 SCALE        = ~SCALE + SCALE;
0129 TYPE         = datatype;
0130 if otherendian == 1 & datatype ~= 2,
0131     TYPE = TYPE*256;
0132 end;
0133 OFFSET          = vox_offset;
0134 ORIGIN        = origin(1:3)';
0135 DESCRIP       = descrip(1:max(find(descrip)));
0136 
0137 else
0138     global DIM VOX SCALE TYPE OFFSET ORIGIN
0139     DESCRIP = ['defaults'];
0140 end
0141 return;
0142 %_______________________________________________________________________
0143 
0144 function out = mysetstr(in)
0145 tmp = find(in == 0);
0146 tmp = min([min(tmp) length(in)]);
0147 out = setstr(in(1:tmp));
0148 return;
spm_hread

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
