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nii_read_header.m
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nii_read_header.m
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function [info] = nii_read_header(filename)
% Function for reading header of NifTi ( .nii ) volume file
%
% Output "info" fields:
% Filesize
% Filename
% SizeofHdr
% Datatype
% DbName
% Extents
% SessionError
% Regular
% DimInfo
% Dimensions
% headerbswap
% IntentP1
% IntentP2
% IntentP3
% IntentCode
% datatypestr
% bitvoxel
% DataTypeStr
% BitVoxel
% Bitpix
% SliceStart
% PixelDimensions
% VoxOffset
% RescaleSlope
% RescaleIntercept
% SliceEnd
% SliceCode
% XyztUnits
% xyzt_unitsstr
% CalMax
% CalMin
% Slice_duration
% Toffset
% Glmax
% Glmin
% Descrip
% AuxFile
% QformCode
% SformCode
% QuaternB
% QuaternC
% QuaternD
% QoffsetX
% QoffsetY
% QoffsetZ
% SrowX
% SrowY
% SrowZ
% IntentName
% Magic
%
% examples:
% 1, info=nii_read_header()
% 2, info=nii_read_header('volume.nii');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.nii', 'Read nii-file');
filename = [pathname filename];
end
bswap=false;
test=true;
while(test)
if(bswap)
fid=fopen(filename,'rb','b');
else
fid=fopen(filename,'rb','l');
end
if(fid<0)
fprintf('could not open file %s\n',filename);
return
end
%get the file size
fseek(fid,0,'eof');
info.Filesize = ftell(fid);
fseek(fid,0,'bof');
info.Filename=filename;
info.SizeofHdr=fread(fid,1,'int');
info.DataType=fread(fid, 10, 'uint8=>char')';
info.DbName=fread(fid, 18, 'uint8=>char')';
info.Extents=fread(fid,1,'int');
info.SessionError=fread(fid,1,'uint16');
info.Regular=fread(fid, 1, 'uint8=>char')';
info.DimInfo=fread(fid, 1, 'uint8=>char')';
swaptemp=fread(fid, 1, 'uint16')';
info.Dimensions=fread(fid,7,'uint16')'; % dim = [ number of dimensions x,y,z,t,c1,c2,c3];
if(swaptemp(1)<1||swaptemp(1)>7), bswap=true; fclose(fid); else test=false; end
end
info.headerbswap=bswap;
info.IntentP1=fread(fid,1,'float');
info.IntentP2=fread(fid,1,'float');
info.IntentP3=fread(fid,1,'float');
info.IntentCode=fread(fid,1,'uint16');
info.DataType=fread(fid,1,'uint16');
datatypestr{1}={0,'UNKNOWN', 0}; % what it says, dude
datatypestr{2}={1,'BINARY', 1}; % binary (1 bit/voxel)
datatypestr{3}={2,'UINT8' , 8};% unsigned char (8 bits/voxel)
datatypestr{4}={4,'INT16' , 16}; % signed short (16 bits/voxel)
datatypestr{5}={8,'INT32' , 32}; % signed int (32 bits/voxel)
datatypestr{6}={16,'FLOAT' , 32}; % float (32 bits/voxel)
datatypestr{7}={32,'COMPLEX', 64}; % complex (64 bits/voxel)
datatypestr{8}={64,'DOUBLE', 64}; % double (64 bits/voxel)
datatypestr{9}={128,'RGB' , 24}; % RGB triple (24 bits/voxel)
datatypestr{10}={255,'ALL' , 0}; % not very useful (?)
datatypestr{11}={256,'INT8' , 8}; % signed char (8 bits)
datatypestr{12}={512,'UINT16', 16}; % unsigned short (16 bits)
datatypestr{13}={768,'UINT32', 32}; % unsigned int (32 bits)
datatypestr{14}={1024,'INT64', 64}; % long long (64 bits)
datatypestr{15}={1280,'UINT64', 64}; % unsigned long long (64 bits)
datatypestr{16}={1536,'FLOAT128', 128}; % long double (128 bits)
datatypestr{17}={1792,'COMPLEX128', 128}; % double pair (128 bits)
datatypestr{18}={2048,'COMPLEX256', 256}; % long double pair (256 bits)
datatypestr{19}={2304,'RGBA32', 32}; % 4 byte RGBA (32 bits/voxel)
info.datatypestr='UNKNOWN';
info.bitvoxel=0;
for i=1:19
if(datatypestr{i}{1}==info.DataType)
info.DataTypeStr=datatypestr{i}{2};
info.BitVoxel=datatypestr{i}{3};
end
end
info.Bitpix=fread(fid,1,'uint16');
info.SliceStart=fread(fid,1,'uint16');
%temp=fread(fid,1,'float');
info.PixelDimensions=fread(fid,8,'float');
info.VoxOffset=fread(fid,1,'float');
info.RescaleSlope=fread(fid,1,'float');
info.RescaleIntercept=fread(fid,1,'float');
info.SliceEnd=fread(fid,1,'uint16');
info.SliceCode=fread(fid, 1, 'uint8=>char')';
info.XyztUnits=fread(fid, 1, 'uint8')';
dataunitsstr{1}={'UNKNOWN', 0}; %! NIFTI code for unspecified units.
dataunitsstr{2}={'METER', 1}; %! NIFTI code for meters.
dataunitsstr{3}={'MM', 2}; %! NIFTI code for millimeters.
dataunitsstr{4}={'MICRON ', 3}; %! NIFTI code for micrometers.
dataunitsstr{5}={'SEC', 8}; %! NIFTI code for seconds.
dataunitsstr{6}={'MSEC', 16}; %! NIFTI code for milliseconds.
dataunitsstr{7}={'USEC', 24}; %! NIFTI code for microseconds.
dataunitsstr{8}={'HZ', 32}; %! NIFTI code for Hertz.
dataunitsstr{9}={'PPM', 40}; %! NIFTI code for ppm.
dataunitsstr{10}={'RADS', 48}; %! NIFTI code for radians per second.
info.xyzt_unitsstr='UNKNOWN';
for i=1:10,
if(dataunitsstr{i}{2}==info.XyztUnits)
info.XyztUnitsStr=dataunitsstr{i}{1};
end
end
info.CalMax=fread(fid,1,'float');
info.CalMin=fread(fid,1,'float');
info.Slice_duration=fread(fid,1,'float');
info.Toffset=fread(fid,1,'float');
info.Glmax=fread(fid,1,'int');
info.Glmin=fread(fid,1,'int');
info.Descrip=fread(fid, 80, 'uint8=>char')';
info.AuxFile=fread(fid, 24, 'uint8=>char')';
info.QformCode=fread(fid,1,'uint16');
info.SformCode=fread(fid,1,'uint16');
info.QuaternB=fread(fid,1,'float');
info.QuaternC=fread(fid,1,'float');
info.QuaternD=fread(fid,1,'float');
info.QoffsetX=fread(fid,1,'float');
info.QoffsetY=fread(fid,1,'float');
info.QoffsetZ=fread(fid,1,'float');
info.SrowX=fread(fid,4,'float');
info.SrowY=fread(fid,4,'float');
info.SrowZ=fread(fid,4,'float');
info.IntentName=fread(fid, 16, 'uint8=>char')';
info.Magic=fread(fid, 4, 'uint8=>char')';
fclose(fid);