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niftiread.m
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niftiread.m
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function str = niftiread (filename)
str.machine = get_machine (filename);
% Lee cabecera
[str.filetype, str.hdr] = leer_cab_nifti(filename, str.machine);
% Lee imagen
str.img = leer_img_nifti (str, filename);
end
function machine = get_machine (filename)
machine = 'ieee-le';
fid = fopen(filename,'r',machine); % supone machine='ieee-le'
if fid < 0, error(['No se puede abrir ' filename]); end
fseek(fid,0,'bof');
if fread(fid,1,'int32') ~= 348 % machine no es correcto
fclose(fid);
machine = 'ieee-be'; % prueba machine='ieee-be'
fid = fopen(filename,'r',machine);
fseek(fid,0,'bof');
if fread(fid,1,'int32') ~= 348
fclose(fid);
fid = -1;
error (['Archivo ' filename ' no válido']);
end
end
fclose(fid);
end
function [filetype, hdr] = leer_cab_nifti (filename, machine)
% Abre el archivo
fid = fopen (filename, 'r', machine);
if fid < 0, error(['No se puede abrir ' filename]); end
fseek (fid,0,'bof');
% Obtiene tipo
fseek (fid, 344, 'bof');
type = deblank(fread(fid,4,'uchar=>char')');
fseek (fid,0,'bof');
filetype = 0;
if strcmp(type, 'ni1'), filetype = 1; end
if strcmp(type, 'n+1'), filetype = 2; end
if filetype == 0
hdr = leer_cab_ana (fid);
else
hdr = leer_cab_nii (fid);
end
fclose(fid);
end
function hdr = leer_cab_nii (fid)
% header_key -> 0-40 -> 40 bytes
hdr.hk.sizeof_hdr = fread(fid, 1,'int32')'; % vale 348
hdr.hk.data_type = deblank(fread(fid,10,'uchar=>char')');
hdr.hk.db_name = deblank(fread(fid,18,'uchar=>char')');
hdr.hk.extents = fread(fid, 1,'int32')';
hdr.hk.session_error = fread(fid, 1,'int16')';
hdr.hk.regular = fread(fid, 1,'uchar=>char')';
hdr.hk.dim_info = fread(fid, 1,'uchar')';
% image_dimension -> 40-148 -> 108 bytes
hdr.dime.dim = fread(fid,8,'int16')';
hdr.dime.intent_p1 = fread(fid,1,'float32')';
hdr.dime.intent_p2 = fread(fid,1,'float32')';
hdr.dime.intent_p3 = fread(fid,1,'float32')';
hdr.dime.intent_code = fread(fid,1,'int16')';
hdr.dime.datatype = fread(fid,1,'int16')';
hdr.dime.bitpix = fread(fid,1,'int16')';
hdr.dime.slice_start = fread(fid,1,'int16')';
hdr.dime.pixdim = abs(fread(fid,8,'float32')');
hdr.dime.vox_offset = fread(fid,1,'float32')';
hdr.dime.scl_slope = fread(fid,1,'float32')';
hdr.dime.scl_inter = fread(fid,1,'float32')';
hdr.dime.slice_end = fread(fid,1,'int16')';
hdr.dime.slice_code = fread(fid,1,'uchar')';
hdr.dime.xyzt_units = fread(fid,1,'uchar')';
hdr.dime.cal_max = fread(fid,1,'float32')';
hdr.dime.cal_min = fread(fid,1,'float32')';
hdr.dime.slice_duration = fread(fid,1,'float32')';
hdr.dime.toffset = fread(fid,1,'float32')';
hdr.dime.glmax = fread(fid,1,'int32')';
hdr.dime.glmin = fread(fid,1,'int32')';
% data_history -> % 148-348 -> 200 bytes
hdr.hist.descrip = deblank(fread(fid,80,'uchar=>char')');
hdr.hist.aux_file = deblank(fread(fid,24,'uchar=>char')');
hdr.hist.qform_code = fread(fid,1,'int16')';
hdr.hist.sform_code = fread(fid,1,'int16')';
hdr.hist.quatern_b = fread(fid,1,'float32')';
hdr.hist.quatern_c = fread(fid,1,'float32')';
hdr.hist.quatern_d = fread(fid,1,'float32')';
hdr.hist.qoffset_x = fread(fid,1,'float32')';
hdr.hist.qoffset_y = fread(fid,1,'float32')';
hdr.hist.qoffset_z = fread(fid,1,'float32')';
hdr.hist.srow_x = fread(fid,4,'float32')';
hdr.hist.srow_y = fread(fid,4,'float32')';
hdr.hist.srow_z = fread(fid,4,'float32')';
hdr.hist.intent_name = deblank(fread(fid,16,'uchar=>char')');
hdr.hist.magic = deblank(fread(fid,4,'uchar=>char')');
end
function hdr = leer_cab_ana (fid)
% header_key -> 0-40 -> 40 bytes
hdr.hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348!
hdr.hk.data_type = deblank(fread(fid,10,'uchar=>char')');
hdr.hk.db_name = deblank(fread(fid,18,'uchar=>char')');
hdr.hk.extents = fread(fid, 1,'int32')';
hdr.hk.session_error = fread(fid, 1,'int16')';
hdr.hk.regular = fread(fid, 1,'uchar=>char')';
hdr.hk.hkey_un0 = fread(fid, 1,'uchar=>char')';
% image_dimension -> 40-148 -> 108 bytes
hdr.dime.dim = fread(fid,8,'int16')';
hdr.dime.vox_units = deblank(fread(fid,4,'uchar=>char')');
hdr.dime.cal_units = deblank(fread(fid,8,'uchar=>char')');
hdr.dime.unused1 = fread(fid,1,'int16')';
hdr.dime.datatype = fread(fid,1,'int16')';
hdr.dime.bitpix = fread(fid,1,'int16')';
hdr.dime.dim_un0 = fread(fid,1,'int16')';
hdr.dime.pixdim = fread(fid,8,'float32')';
hdr.dime.vox_offset = fread(fid,1,'float32')';
hdr.dime.roi_scale = fread(fid,1,'float32')';
hdr.dime.funused1 = fread(fid,1,'float32')';
hdr.dime.funused2 = fread(fid,1,'float32')';
hdr.dime.cal_max = fread(fid,1,'float32')';
hdr.dime.cal_min = fread(fid,1,'float32')';
hdr.dime.compressed = fread(fid,1,'int32')';
hdr.dime.verified = fread(fid,1,'int32')';
hdr.dime.glmax = fread(fid,1,'int32')';
hdr.dime.glmin = fread(fid,1,'int32')';
% data_history -> % 148-348 -> 200 bytes
hdr.hist.descrip = deblank(fread(fid,80,'uchar=>char')');
hdr.hist.aux_file = deblank(fread(fid,24,'uchar=>char')');
hdr.hist.orient = fread(fid, 1,'char')';
hdr.hist.originator = fread(fid, 5,'int16')';
hdr.hist.generated = deblank(fread(fid,10,'uchar=>char')');
hdr.hist.scannum = deblank(fread(fid,10,'uchar=>char')');
hdr.hist.patient_id = deblank(fread(fid,10,'uchar=>char')');
hdr.hist.exp_date = deblank(fread(fid,10,'uchar=>char')');
hdr.hist.exp_time = deblank(fread(fid,10,'uchar=>char')');
hdr.hist.hist_un0 = deblank(fread(fid, 3,'uchar=>char')');
hdr.hist.views = fread(fid, 1,'int32')';
hdr.hist.vols_added = fread(fid, 1,'int32')';
hdr.hist.start_field = fread(fid, 1,'int32')';
hdr.hist.field_skip = fread(fid, 1,'int32')';
hdr.hist.omax = fread(fid, 1,'int32')';
hdr.hist.omin = fread(fid, 1,'int32')';
hdr.hist.smax = fread(fid, 1,'int32')';
hdr.hist.smin = fread(fid, 1,'int32')';
end
function img = leer_img_nifti (str, filename)
if str.filetype == 2;
imgname = filename;
offset = str.hdr.dime.vox_offset;
else
[r n] = fileparts (filename);
imgname = fullfile(r, [n '.img']);
offset = 0;
end
fid = fopen (imgname, 'r', str.machine);
if fid < 0, error(['No se puede abrir ' imgname]); end
fseek (fid, offset, 'bof');
% Determina precision (ps) y numero de capas (nl)
datatype = uint16(str.hdr.dime.datatype);
[ps, nl] = get_type (datatype);
if isempty (ps), error ('Tipo de datos no válido'); end
% Lee todos los voxeles
str.hdr.dime.dim (str.hdr.dime.dim < 1) = 1;
nbytes = prod (str.hdr.dime.dim(2:8)) * nl;
[img, count] = fread (fid, nbytes, ['*' ps]);
if count < nbytes, error(['Archivo ' imgname ' truncado']); end
% Si hay varias capas (para colores)
if datatype == 128 || datatype == 2304
img = reshape(img, [nl str.hdr.dime.dim(2:8)]);
img = permute(img, [2 3 4 1 5 6 7 8]);
% Numeros complejos (2 capas, una para parte real y otra para imag)
elseif datatype == 32 || datatype == 1792 || datatype == 2048
parte_real = 1:2:numel(img);
parte_imag = 2:2:numel(img);
img = complex (img(parte_real), img(parte_imag));
img = reshape(img, str.hdr.dime.dim(2:8));
else
img = reshape(img, str.hdr.dime.dim(2:8));
end
fclose (fid);
end
function [ps, nl] = get_type (datatype)
switch datatype
% ANALYZE 7.5 type codes
case 1, ps = 'ubit1'; nl = 1; % binary (1 bit/voxel)
case 2, ps = 'uint8'; nl = 1; % unsigned char (8 bits/voxel)
case 4, ps = 'int16'; nl = 1; % signed short (16 bits/voxel)
case 8, ps = 'int32'; nl = 1; % signed int (32 bits/voxel)
case 16, ps = 'float32'; nl = 1; % float (32 bits/voxel)
case 32, ps = 'float32'; nl = 2; % complex (64 bits/voxel)
case 64, ps = 'float64'; nl = 1; % double (64 bits/voxel)
case 128, ps = 'uint8'; nl = 3; % RGB triple (24 bits/voxel)
% new codes for NIFTI
case 256, ps = 'int8'; nl = 1; % signed char (8 bits)
case 512, ps = 'uint16'; nl = 1; % unsigned short (16 bits)
case 768, ps = 'uint32'; nl = 1; % unsigned int (32 bits)
case 1024, ps = 'int64'; nl = 1; % long long (64 bits)
case 1280, ps = 'uint64'; nl = 1; % unsigned long long (64 bits)
case 1536, ps = 'bit128=>float64'; nl = 1; % long double (128 bits)
case 1792, ps = 'float64'; nl = 2; % double pair (128 bits)
case 2048, ps = 'bit128=>float64'; nl = 2; % long double pair (256 bits)
case 2304, ps = 'uint8'; nl = 4; % RGBA (32 bits/voxel)
otherwise, ps = ''; nl = 1;
end
end