read_nifti

 Create a NIFTI-1 object
 _______________________________________________________________________
 Copyright (C) 2005 Wellcome Department of Imaging Neuroscience

0001 function h = read_nifti(varargin)
0002 % Create a NIFTI-1 object
0003 % _______________________________________________________________________
0004 % Copyright (C) 2005 Wellcome Department of Imaging Neuroscience
0005 
0006 %
0007 % $Id: nifti.m 253 2005-10-13 15:31:34Z guillaume $
0008 
0009 
0010 switch nargin
0011 case 0,
0012     org = niftistruc;
0013     hdr = [];
0014     for i=1:length(org),
0015         hdr.(org(i).label) = feval(org(i).dtype.conv,org(i).def);
0016     end;
0017     h = struct('hdr',hdr,'dat',[],'extras',struct);
0018     h = class(h,'read_nifti');
0019 
0020 case 1
0021     if ischar(varargin{1})
0022         if size(varargin{1},1)>1,
0023             h = read_nifti(cellstr(varargin{1}));
0024             return;
0025         end;
0026         fname  = deblank(varargin{1});
0027         vol    = read_hdr(fname);
0028         extras = read_extras(fname);
0029 
0030         if ~isfield(vol.hdr,'magic'),
0031             vol.hdr = mayo2nifti1(vol.hdr);
0032 
0033             % For SPM99 compatibility
0034             if isfield(extras,'M') && ~isfield(extras,'mat'),
0035                  extras.mat = extras.M;
0036                  if nc_spm_flip_analyze_images,
0037                      extras.mat = diag([-1 1 1 1])*extras.mat;
0038                  end;
0039             end;
0040 
0041             % Over-ride sform if a .mat file exists
0042             if isfield(extras,'mat') && size(extras.mat,3)>=1,
0043                 mat            = extras.mat(:,:,1);
0044                 mat1           = mat*[eye(4,3) [1 1 1 1]'];
0045                 vol.hdr.srow_x = mat1(1,:);
0046                 vol.hdr.srow_y = mat1(2,:);
0047                 vol.hdr.srow_z = mat1(3,:);
0048                 vol.hdr.sform_code = 2;
0049                 vol.hdr.qform_code = 2;
0050                 vol.hdr = encode_qform0(mat,vol.hdr);
0051             end;
0052         end;
0053 
0054         if isfield(extras,'M'), extras = rmfield(extras,'M'); end;
0055         if isfield(extras,'mat') && size(extras.mat,3)<=1,
0056             extras = rmfield(extras,'mat');
0057         end;
0058 
0059         dim   = double(vol.hdr.dim);
0060         dim   = dim(2:(dim(1)+1));
0061         dt    = double(vol.hdr.datatype);
0062         offs  = double(vol.hdr.vox_offset);
0063 
0064         if ~vol.hdr.scl_slope && ~vol.hdr.scl_inter,
0065             vol.hdr.scl_slope = 1;
0066         end;
0067         slope = double(vol.hdr.scl_slope);
0068         inter = double(vol.hdr.scl_inter);
0069 
0070         dat   = create_file_array(vol.iname,dim,[dt,vol.be],offs,slope,inter);
0071         h     = struct('hdr',vol.hdr,'dat',dat,'extras',extras);
0072         h     = class(h,'read_nifti');
0073 
0074     elseif isstruct(varargin{1})
0075         h     = class(varargin{1},'read_nifti');
0076 
0077     elseif iscell(varargin{1})
0078         fnames = varargin{1};
0079         h(numel(fnames)) = struct('hdr',[],'dat',[],'extras',struct);
0080         h     = class(h,'read_nifti');
0081         for i=1:numel(fnames),
0082             h(i) = read_nifti(fnames{i});
0083         end;
0084 
0085     else
0086         error('Dont know what to do yet.');
0087     end;
0088 otherwise
0089     error('Dont know what to do yet');
0090 end;
0091 return;