Feb 082010
I am always look for different MRI file readers and writers for the myriad of formats that we use in MRI research. One of the relatively simple and common ones is the Analyze fileformat. Some of the large packages have writers (e.g., SPM) but I am typically wanting to do my own small processing and then write out the data. So, I wrote up my own writeanalyze.m function. It will do the basic formatting though the offsets etc don’t work. Try it out but I can’t guarantee anything.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 | function [] = writeanalyze(fname, data, ftype) if( nargin == 2 ) ftype = 'int16'; end if( strcmp( ftype, 'int16' ) == 1 ) file_type = 4; bpp = 16; elseif( strcmp( ftype, 'uint16' ) == 1 ) file_type = 4; bpp = 16; elseif( strcmp( ftype, 'int32' ) == 1 ) file_type = 8; bpp = 32; elseif( strcmp( ftype, 'float' ) == 1 ) file_type = 16; bpp = 32; elseif( strcmp( ftype, 'double' ) == 1 ) file_type = 64; bpp = 64; else error(sprintf('Unknown data type %s', ftype)); end fp = fopen([fname '.hdr'], 'wb', 'b'); %% %% Write the header_key part %% fwrite(fp, 348, 'int32'); fwrite(fp, repmat(' ', 1, 10), 'char'); fwrite(fp, repmat(' ', 1, 18), 'char'); fwrite(fp, 16384, 'int32'); fwrite(fp, 0, 'int16'); fwrite(fp, 'r ', 'char'); %% %% Write the image_dimension part. %% fwrite(fp, length( size(data) ), 'int16'); for ii=1:length( size(data) ) fwrite(fp, size(data,ii), 'int16'); end for ii=length( size(data) )+1:7 fwrite(fp, 1, 'int16'); end fwrite(fp, 0, 'int16'); % unused 8 fwrite(fp, 0, 'int16'); % unused 9 fwrite(fp, 0, 'int16'); % unused 10 fwrite(fp, 0, 'int16'); % unused 11 fwrite(fp, 0, 'int16'); % unused 12 fwrite(fp, 0, 'int16'); % unused 13 fwrite(fp, 0, 'int16'); % unused 14 % data type fwrite(fp, file_type, 'int16'); % 4 = signed short fwrite(fp, bpp, 'int16'); % bpp fwrite(fp, 0, 'int16'); for ii=1:8 fwrite(fp, 1.0, 'float32'); end fwrite(fp, 0, 'float32'); fwrite(fp, 0, 'float32'); % funused 1 fwrite(fp, 0, 'float32'); % funused 2 fwrite(fp, 0, 'float32'); % funused 3 fwrite(fp, max(data(:)), 'float32'); fwrite(fp, min(data(:)), 'float32'); fwrite(fp, 0, 'float32'); fwrite(fp, 0, 'float32'); fwrite(fp, round(max(data(:))), 'int32'); % glmax fwrite(fp, round(min(data(:))), 'int32'); % glmin %% %% Data history %% fwrite(fp, repmat(' ', 1, 80), 'char'); % descrip fwrite(fp, repmat(' ', 1, 24), 'char'); % aux_file fwrite(fp, '3', 'char'); % aux_file fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 10), 'char'); % originator fwrite(fp, repmat(' ', 1, 3), 'char'); % originator fwrite(fp, 0, 'int32'); % views fwrite(fp, 0, 'int32'); % vols_added fwrite(fp, 0, 'int32'); % start_fiedl fwrite(fp, 0, 'int32'); % field_skip fwrite(fp, 0, 'int32'); % omax fwrite(fp, 0, 'int32'); % omin fwrite(fp, 0, 'int32'); % small_max fwrite(fp, 0, 'int32'); % small_min fclose(fp); %% %% Write the data %% fp = fopen([fname '.img'], 'wb', 'b'); fwrite(fp, data, ftype); fclose(fp); |
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