save_nii_hdr_cbi

  Save NIFTI dataset header. Support both *.nii and *.hdr/*.img file
  extension.
  
  Usage: save_nii_hdr(hdr, fid)
  
  hdr - struct with NIFTI header fields.
  
  fileprefix - NIFTI file name without extension.
  
  Part of this file is copied and modified under GNU license from
  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
  
  NIFTI data format can be found on: http://nifti.nimh.nih.gov
  
  - Jimmy Shen (pls@rotman-baycrest.on.ca)

0001 %  Save NIFTI dataset header. Support both *.nii and *.hdr/*.img file
0002 %  extension.
0003 %
0004 %  Usage: save_nii_hdr(hdr, fid)
0005 %
0006 %  hdr - struct with NIFTI header fields.
0007 %
0008 %  fileprefix - NIFTI file name without extension.
0009 %
0010 %  Part of this file is copied and modified under GNU license from
0011 %  MRI_TOOLBOX developed by CNSP in Flinders University, Australia
0012 %
0013 %  NIFTI data format can be found on: http://nifti.nimh.nih.gov
0014 %
0015 %  - Jimmy Shen (pls@rotman-baycrest.on.ca)
0016 %
0017 function save_nii_hdr(hdr, fid)
0018    
0019    if ~exist('hdr','var') | ~exist('fid','var')
0020       error('Usage: save_nii_hdr(hdr, fid)');
0021    end
0022    
0023    if ~isequal(hdr.hk.sizeof_hdr,348),
0024       error('hdr.hk.sizeof_hdr must be 348.');
0025    end
0026    
0027    if hdr.hist.qform_code == 0 & hdr.hist.sform_code == 0
0028       hdr.hist.sform_code = 1;
0029       hdr.hist.srow_x(1) = hdr.dime.pixdim(2);
0030       hdr.hist.srow_x(2) = 0;
0031       hdr.hist.srow_x(3) = 0;
0032       hdr.hist.srow_y(1) = 0;
0033       hdr.hist.srow_y(2) = hdr.dime.pixdim(3);
0034       hdr.hist.srow_y(3) = 0;
0035       hdr.hist.srow_z(1) = 0;
0036       hdr.hist.srow_z(2) = 0;
0037       hdr.hist.srow_z(3) = hdr.dime.pixdim(4);
0038       hdr.hist.srow_x(4) = (1-hdr.hist.originator(1))*hdr.dime.pixdim(2);
0039       hdr.hist.srow_y(4) = (1-hdr.hist.originator(2))*hdr.dime.pixdim(3);
0040       hdr.hist.srow_z(4) = (1-hdr.hist.originator(3))*hdr.dime.pixdim(4);
0041    end
0042    
0043    write_header(hdr, fid);
0044 
0045    return;                    % save_nii_hdr
0046 
0047 
0048 %---------------------------------------------------------------------
0049 function write_header(hdr, fid)
0050 
0051         %  Original header structures
0052     %  struct dsr                /* dsr = hdr */
0053     %       {
0054     %       struct header_key hk;            /*   0 +  40       */
0055     %       struct image_dimension dime;     /*  40 + 108       */
0056     %       struct data_history hist;        /* 148 + 200       */
0057     %       };                               /* total= 348 bytes*/
0058    
0059    header_key(fid, hdr.hk);
0060    image_dimension(fid, hdr.dime);
0061    data_history(fid, hdr.hist);
0062    
0063    %  check the file size is 348 bytes
0064    %
0065    fbytes = ftell(fid);
0066    
0067    if ~isequal(fbytes,348),
0068       msg = sprintf('Header size is not 348 bytes.');
0069       warning(msg);
0070    end
0071     
0072    return;                    % write_header
0073 
0074 
0075 %---------------------------------------------------------------------
0076 function header_key(fid, hk)
0077    
0078    fseek(fid,0,'bof');
0079 
0080     %  Original header structures
0081     %  struct header_key                      /* header key      */
0082     %       {                                /* off + size      */
0083     %       int sizeof_hdr                   /*  0 +  4         */
0084     %       char data_type[10];              /*  4 + 10         */
0085     %       char db_name[18];                /* 14 + 18         */
0086     %       int extents;                     /* 32 +  4         */
0087     %       short int session_error;         /* 36 +  2         */
0088     %       char regular;                    /* 38 +  1         */
0089     %       char dim_info;   % char hkey_un0;        /* 39 +  1 */
0090     %       };                               /* total=40 bytes  */
0091         
0092    fwrite(fid, hk.sizeof_hdr(1),    'int32');    % must be 348.
0093     
0094    % data_type = sprintf('%-10s',hk.data_type);    % ensure it is 10 chars from left
0095    % fwrite(fid, data_type(1:10), 'uchar');
0096    pad = zeros(1, 10-length(hk.data_type));
0097    hk.data_type = [hk.data_type  char(pad)];
0098    fwrite(fid, hk.data_type(1:10), 'uchar');
0099     
0100    % db_name   = sprintf('%-18s', hk.db_name);    % ensure it is 18 chars from left
0101    % fwrite(fid, db_name(1:18), 'uchar');
0102    pad = zeros(1, 18-length(hk.db_name));
0103    hk.db_name = [hk.db_name  char(pad)];
0104    fwrite(fid, hk.db_name(1:18), 'uchar');
0105     
0106    fwrite(fid, hk.extents(1),       'int32');
0107    fwrite(fid, hk.session_error(1), 'int16');
0108    fwrite(fid, hk.regular(1),       'uchar');    % might be uint8
0109     
0110    % fwrite(fid, hk.hkey_un0(1),    'uchar');
0111    % fwrite(fid, hk.hkey_un0(1),    'uint8');
0112    fwrite(fid, hk.dim_info(1),      'uchar');
0113     
0114    return;                    % header_key
0115 
0116 
0117 %---------------------------------------------------------------------
0118 function image_dimension(fid, dime)
0119 
0120     %  Original header structures
0121     %  struct image_dimension
0122     %       {                                /* off + size      */
0123     %       short int dim[8];                /* 0 + 16          */
0124     %       float intent_p1;   % char vox_units[4];   /* 16 + 4       */
0125     %       float intent_p2;   % char cal_units[8];   /* 20 + 4       */
0126     %       float intent_p3;   % char cal_units[8];   /* 24 + 4       */
0127     %       short int intent_code;   % short int unused1;   /* 28 + 2 */
0128     %       short int datatype;              /* 30 + 2          */
0129     %       short int bitpix;                /* 32 + 2          */
0130     %       short int slice_start;   % short int dim_un0;   /* 34 + 2 */
0131     %       float pixdim[8];                 /* 36 + 32         */
0132     %            /*
0133     %                pixdim[] specifies the voxel dimensions:
0134     %                pixdim[1] - voxel width
0135     %                pixdim[2] - voxel height
0136     %                pixdim[3] - interslice distance
0137     %                pixdim[4] - volume timing, in msec
0138     %                    ..etc
0139     %            */
0140     %       float vox_offset;                /* 68 + 4          */
0141     %       float scl_slope;   % float roi_scale;     /* 72 + 4 */
0142     %       float scl_inter;   % float funused1;      /* 76 + 4 */
0143     %       short slice_end;   % float funused2;      /* 80 + 2 */
0144     %       char slice_code;   % float funused2;      /* 82 + 1 */
0145     %       char xyzt_units;   % float funused2;      /* 83 + 1 */
0146     %       float cal_max;                   /* 84 + 4          */
0147     %       float cal_min;                   /* 88 + 4          */
0148     %       float slice_duration;   % int compressed; /* 92 + 4 */
0149     %       float toffset;   % int verified;          /* 96 + 4 */
0150     %       int glmax;                       /* 100 + 4         */
0151     %       int glmin;                       /* 104 + 4         */
0152     %       };                               /* total=108 bytes */
0153     
0154    fwrite(fid, dime.dim(1:8),        'int16');
0155    fwrite(fid, dime.intent_p1(1),  'float32');
0156    fwrite(fid, dime.intent_p2(1),  'float32');
0157    fwrite(fid, dime.intent_p3(1),  'float32');
0158    fwrite(fid, dime.intent_code(1),  'int16');
0159    fwrite(fid, dime.datatype(1),     'int16');
0160    fwrite(fid, dime.bitpix(1),       'int16');
0161    fwrite(fid, dime.slice_start(1),  'int16');
0162    fwrite(fid, dime.pixdim(1:8),   'float32');
0163    fwrite(fid, dime.vox_offset(1), 'float32');
0164    fwrite(fid, dime.scl_slope(1),  'float32');
0165    fwrite(fid, dime.scl_inter(1),  'float32');
0166    fwrite(fid, dime.slice_end(1),    'int16');
0167    fwrite(fid, dime.slice_code(1),   'uchar');
0168    fwrite(fid, dime.xyzt_units(1),   'uchar');
0169    fwrite(fid, dime.cal_max(1),    'float32');
0170    fwrite(fid, dime.cal_min(1),    'float32');
0171    fwrite(fid, dime.slice_duration(1), 'float32');
0172    fwrite(fid, dime.toffset(1),    'float32');
0173    fwrite(fid, dime.glmax(1),        'int32');
0174    fwrite(fid, dime.glmin(1),        'int32');
0175    
0176    return;                    % image_dimension
0177 
0178 
0179 %---------------------------------------------------------------------
0180 function data_history(fid, hist)
0181     
0182     % Original header structures
0183     %struct data_history
0184     %       {                                /* off + size      */
0185     %       char descrip[80];                /* 0 + 80          */
0186     %       char aux_file[24];               /* 80 + 24         */
0187     %       short int qform_code;            /* 104 + 2         */
0188     %       short int sform_code;            /* 106 + 2         */
0189     %       float quatern_b;                 /* 108 + 4         */
0190     %       float quatern_c;                 /* 112 + 4         */
0191     %       float quatern_d;                 /* 116 + 4         */
0192     %       float qoffset_x;                 /* 120 + 4         */
0193     %       float qoffset_y;                 /* 124 + 4         */
0194     %       float qoffset_z;                 /* 128 + 4         */
0195     %       float srow_x[4];                 /* 132 + 16        */
0196     %       float srow_y[4];                 /* 148 + 16        */
0197     %       float srow_z[4];                 /* 164 + 16        */
0198     %       char intent_name[16];            /* 180 + 16        */
0199     %       char magic[4];   % int smin;     /* 196 + 4         */
0200     %       };                               /* total=200 bytes */
0201     
0202    % descrip     = sprintf('%-80s', hist.descrip);     % 80 chars from left
0203    % fwrite(fid, descrip(1:80),    'uchar');
0204    pad = zeros(1, 80-length(hist.descrip));
0205    hist.descrip = [hist.descrip  char(pad)];
0206    fwrite(fid, hist.descrip(1:80), 'uchar');
0207     
0208    % aux_file    = sprintf('%-24s', hist.aux_file);    % 24 chars from left
0209    % fwrite(fid, aux_file(1:24),   'uchar');
0210    pad = zeros(1, 24-length(hist.aux_file));
0211    hist.aux_file = [hist.aux_file  char(pad)];
0212    fwrite(fid, hist.aux_file(1:24), 'uchar');
0213     
0214    fwrite(fid, hist.qform_code,    'int16');
0215    fwrite(fid, hist.sform_code,    'int16');
0216    fwrite(fid, hist.quatern_b,   'float32');
0217    fwrite(fid, hist.quatern_c,   'float32');
0218    fwrite(fid, hist.quatern_d,   'float32');
0219    fwrite(fid, hist.qoffset_x,   'float32');
0220    fwrite(fid, hist.qoffset_y,   'float32');
0221    fwrite(fid, hist.qoffset_z,   'float32');
0222    fwrite(fid, hist.srow_x(1:4), 'float32');
0223    fwrite(fid, hist.srow_y(1:4), 'float32');
0224    fwrite(fid, hist.srow_z(1:4), 'float32');
0225 
0226    % intent_name = sprintf('%-16s', hist.intent_name);    % 16 chars from left
0227    % fwrite(fid, intent_name(1:16),    'uchar');
0228    pad = zeros(1, 16-length(hist.intent_name));
0229    hist.intent_name = [hist.intent_name  char(pad)];
0230    fwrite(fid, hist.intent_name(1:16), 'uchar');
0231     
0232    % magic    = sprintf('%-4s', hist.magic);        % 4 chars from left
0233    % fwrite(fid, magic(1:4),           'uchar');
0234    pad = zeros(1, 4-length(hist.magic));
0235    hist.magic = [hist.magic  char(pad)];
0236    fwrite(fid, hist.magic(1:4),        'uchar');
0237     
0238    return;                    % data_history
0239