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iCAPs/packages/cbiNifti/cbiCreateNiftiHeader.m
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cbiCreateNiftiHeader.m
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function hdr=cbiCreateNiftiHeader(varargin)
% hdr=cbiCreateNiftiHeader(varargin)
%
% Generates a NIFTI-compatible Matlab header struct that can be saved with cbiWriteNiftiHeader.
%
% SYNTAX:
% hdr=cbiCreateNiftiHeader
% No input arguments: generates a bare-bone header struct with correctly sized fields.
% Sets endianness and default data type (float), with voxel size=1 mm isotropic.
% hdr=cbiCreateNiftiHeader(data)
% Input is a data array: generates a header to match data (essentially as option (1) but also sets hdr.dims)
% hdr=cbiCreateNiftiHeader(hdr)
% Input is a header struct: adds missing fields to an existing header and ensures consistency.
% hdr=cbiCreateNiftiHeader(hdr_field1,value1,hdr_field2,value2,...)
% Input is a set of parameter-value pairs, e.g. ( 'srow_x', [0 0 0 1] ). Sets the corresponding field.
%
% The output is checked to make sure it is consistent (within limits). Specifically:
% - If a data array is given as input, hdr.dim will be set from this (overriding parameter-value pairs)
% - Quaternions will be set as follows:
% a) if neither qform44, or quatern_[b/c/d] are specified, will use existing hdr info
% (if valid, qform44 takes precedence over quaternions)
% b) specifying a quaternion/qoffset as a parameter sets qform44 accordingly
% c) specifying a qform44 sets quaternions accordingly (overriding any quaternion parameters)
% d) if qform44 is empty, qform_code=0, else qform_code=1
% - Sform data will be set as follows:
% - a) if neither sform44 or srow_[x/y/z] are specified, will use existing hdr info
% (if valid, sform44 takes precedence over srow_[x/y/z]
% - b) specifying a srow_ paramater sets sform44 accordingly
% - c) specifying sform44 sets srows accordingly (overriding any srow parameters)
% - d) if sform44 is empty, sform_code=0, else sform_code=1
% - Setting the matlab_datatype also sets the NIFTI data type and bitpix appropriately (and vice versa).
% (note: bitpix is determined by the datatype; setting it directly has no effect)
% - Setting the file name also sets the magic number
%
% Options 2-4 can be combined. The data and header input arguments must come before the parameter-value pairs.
if (nargin==0)
% create empty header
hdr=generateEmptyNiftiHeader;
return
end
% Check if the input contains a data or existing header struct
input_hdr=0;
input_data=0;
for currarg=1:min([nargin;2])
if (isstruct(varargin{currarg}))
input_hdr=currarg;
elseif (~isstr(varargin{currarg}))
if (currarg==1)
% must be a data array - parameter/value pairs always start with a string
input_data=currarg;
else
% can only be a data array if the first argument was the header
if (input_hdr==1)
input_data=currarg;
end
end
end
end
% Make a header
if (input_hdr)
hdr=generateEmptyNiftiHeader(varargin{input_hdr});
else
hdr=generateEmptyNiftiHeader;
end
use_quatern=0;
use_qform=0;
use_srow=0;
use_sform=0;
% Set parameter-value pairs
argstart=max([input_hdr input_data])+1;
if (argstart<nargin)
if (rem(nargin-argstart+1,2))
error('Missing value for parameter-value pairs');
end
for currarg=argstart:2:nargin
if (~isstr(varargin{currarg}))
error('Incorrect parameter specification (expected a field name)');
end
hdr=setfield(hdr,varargin{currarg},varargin{currarg+1});
if ~isempty(findstr('srow',varargin{currarg}))
use_srow=1;
end
if ~isempty(findstr('sform44',varargin{currarg}))
use_sform=1;
end
if (~isempty(findstr('quatern',varargin{currarg})) | ~isempty(findstr('qoffset',varargin{currarg})))
use_quatern=1;
end
if ~isempty(findstr('qform44',varargin{currarg}))
use_qform=1;
end
if strcmp(varargin{currarg},'datatype')
hdr.matlab_datatype=cbiNiftiDatatype2Matlab(hdr.datatype);
end
if strcmp(varargin{currarg},'matlab_datatype')
hdr.datatype=cbiMatlabDatatype2Nifti(hdr.matlab_datatype);
end
end
end
if (use_qform)
use_quatern=0;
end
if (use_sform)
use_srow=0;
end
if (~use_qform & ~use_quatern)
use_qform=1;
end
if (~use_sform & ~use_srow)
use_sform=1;
end
% Set data size, if any
if (input_data)
s=size(varargin{input_data});
l=length(s);
hdr.dim(1)=l;
hdr.dim(2:l+1)=s;
hdr.slice_end=s(3)-1; % dim3 (Z) is slice direction
% Set pixdim fields, if not set
for n=2:l+1
if (hdr.pixdim(n)==0)
hdr.pixdim(n)=1;
end
end
end
if (use_quatern)
% Make sure quaternions are valid
quatern=[hdr.quatern_b hdr.quatern_c hdr.quatern_d];
pixdim=hdr.pixdims(2:4);
qfac=hdr.pixdims(1);
qoffs=[hdr.qoffset_x;hdr.qoffset_y;hdr.qoffset_z];
if (length(quatern)==3 & length(qoffs)==3 & prod(pixdim)~=0)
% Calculate qform44
hdr.qform44=cbiQuaternionToHomogeneous( quatern, pixdim, qfac, qoffset );
else
% Else set all to null values
hdr.quatern_b=0;
hdr.quatern_c=0;
hdr.quatern_d=0;
hdr.qoffset_x=0;
hdr.qoffset_y=0;
hdr.qoffset_z=0;
hdr.qform44=[];
end
end
if (use_qform)
% Make sure qform44 is valid
if (~isempty(hdr.qform44) & ~isequal(hdr.qform44,eye(4)) & ~isequal(hdr.qform44,zeros(4,4)) & size(hdr.qform44)==[4,4])
hdr=cbiSetNiftiQform( hdr, hdr.qform44 );
else
% Else set all to null values
hdr.quatern_b=0;
hdr.quatern_c=0;
hdr.quatern_d=0;
hdr.qoffset_x=0;
hdr.qoffset_y=0;
hdr.qoffset_z=0;
hdr.qform44=[];
end
end
if (use_srow)
% Make sure srows are valid
if (length(hdr.srow_x)==4 & length(hdr.srow_y)==4 & length(hdr.srow_z)==4 )
% Calculate sform44
hdr.sform44=eye(4);
hdr.sform44(1,:)=hdr.srow_x;
hdr.sform44(2,:)=hdr.srow_y;
hdr.sform44(3,:)=hdr.srow_z;
else
% Else set all to null values
hdr.srow_x=zeros(1,4);
hdr.srow_y=zeros(1,4);
hdr.srow_z=zeros(1,4);
hdr.sform44=[];
end
end
if (use_sform)
% Make sure sform44 are valid
if (~isempty(hdr.sform44) & ~isequal(hdr.sform44,eye(4)) & ~isequal(hdr.sform44,zeros(4)) & size(hdr.sform44)==[4,4])
% Calculate srows
hdr.srow_x=hdr.sform44(1,:);
hdr.srow_y=hdr.sform44(2,:);
hdr.srow_z=hdr.sform44(3,:);
else
% Else set all to null values
hdr.srow_x=zeros(1,4);
hdr.srow_y=zeros(1,4);
hdr.srow_z=zeros(1,4);
hdr.sform44=[];
end
end
% Set qform_code, sform_code according to header
% qform44:
if (~isempty(hdr.qform44))
hdr.qform_code=1;
else
hdr.qform_code=0;
end
% sform44:
if (~isempty(hdr.sform44))
hdr.sform_code=1;
else
hdr.sform_code=0;
end
% file name: set magic number
if (isfield(hdr,'hdr_name'))
[pathstr,bname,ext]=fileparts(hdr.hdr_name);
switch (ext)
case '.nii'
hdr.single_file=1;
hdr.magic='n+1';
case {'.hdr','.img'}
hdr.single_file=0;
hdr.magic='ni1';
otherwise
disp('Warning: unrecognized file name field.');
end
end
% Truncate char arrays
if (length(hdr.aux_file)>24)
hdr.aux_file=hdr.aux_file(1:24);
else
hdr.aux_file=[hdr.aux_file char(zeros(1,24-length(hdr.aux_file)))];
end
if (length(hdr.descrip)>80)
hdr.descrip=hdr.descrip(1:80);
else
hdr.descrip=[hdr.descrip char(zeros(1,80-length(hdr.descrip)))];
end
if (length(hdr.intent_name)>16)
hdr.intent_name=hdr.intent_name(1:16);
else
hdr.intent_name=[hdr.intent_name char(zeros(1,16-length(hdr.intent_name)))];
end
return
function h=generateEmptyNiftiHeader(h)
if (~exist('h'))
h=[];
end
% For every header field, check if it exists, otherwise add it
h.sizeof_hdr=348;
if (~isfield(h,'dim_info'))
h.dim_info=' ';
end
if (~isfield(h,'dim'))
h.dim=zeros(8,1);
end
if (~isfield(h,'intent_ps'))
h.intent_ps=zeros(3,1);
end
if (~isfield(h,'intent_code'))
h.intent_code=0;
end
if (~isfield(h,'endian'))
h.endian='native';
end
if (~isfield(h,'datatype'))
h.datatype=16;
end
h.matlab_datatype=cbiNiftiDatatype2Matlab(h.datatype);
h.bitpix=8*cbiSizeofNifti(h.matlab_datatype);
if (~isfield(h,'slice_start'))
h.slice_start=0;
end
if (~isfield(h,'slice_end'))
h.slice_end=0;
end
if (~isfield(h,'pixdim'))
h.pixdim=zeros(8,1);
end
if (~isfield(h,'vox_offset'))
h.vox_offset=0;
end
if (~isfield(h,'scl_slope'))
h.scl_slope=1;
end
if (~isfield(h,'scl_inter'))
h.scl_inter=0;
end
if (~isfield(h,'slice_code'))
h.slice_code=0;
end
if (~isfield(h,'xyzt_units'))
h.xyzt_units=18; % NIFTI_UNITS_MM | NIFTI_UNITS_SEC
end
if (~isfield(h,'cal_max'))
h.cal_max=0;
end
if (~isfield(h,'cal_min'))
h.cal_min=0;
end
if (~isfield(h,'slice_duration'))
h.slice_duration=0;
end
if (~isfield(h,'toffset'))
h.toffset=0;
end
if (~isfield(h,'descrip'))
h.descrip=char(zeros(1,80));
end
if (~isfield(h,'aux_file'))
h.aux_file=char(zeros(1,24));
end
if (~isfield(h,'qform_code'))
h.qform_code=0;
end
if (~isfield(h,'sform_code'))
h.sform_code=0;
end
if (~isfield(h,'quatern_b'))
h.quatern_b=0;
end
if (~isfield(h,'quatern_c'))
h.quatern_c=0;
end
if (~isfield(h,'quatern_d'))
h.quatern_d=0;
end
if (~isfield(h,'qoffset_x'))
h.qoffset_x=0;
end
if (~isfield(h,'qoffset_y'))
h.qoffset_y=0;
end
if (~isfield(h,'qoffset_z'))
h.qoffset_z=0;
end
if (~isfield(h,'srow_x'))
h.srow_x=[0 0 0 0];
end
if (~isfield(h,'srow_y'))
h.srow_y=[0 0 0 0];
end
if (~isfield(h,'srow_z'))
h.srow_z=[0 0 0 0];
end
if (~isfield(h,'intent_name'))
h.intent_name=char(zeros(1,16));
end
if (~isfield(h,'magic'))
h.magic='';
end
if (~isfield(h,'qform44'))
h.qform44=[];
end
if (~isfield(h,'sform44'))
h.sform44=[];
end
if (~isfield(h,'intent_ps'))
h.intent_ps=zeros(3,1);
end
return
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