Write ANALYZE 7.5 or NIFTI file by YAN Chao-Gan
FORMAT function [] = rest_writefile(data,filename,isize,vsize,dtype)
data - data file.
filename - Analyze or NIFTI file (*.{hdr, img, nii})
isize - the size of the data
vsize - the size of the voxel
dtype - the data type.
Header - It will decide to write ANALYZE7.5 or NIFTI file by
whether Header has the field 'mat'.
Analyze format - Header just has one subfield: Header.Origin - the origin of the images.
NIFTI format - Head.fname - the filename of the image.
Head.dim - the x, y and z dimensions of the volume
Head.dt - A 1x2 array. First element is datatype (see spm_type).
The second is 1 or 0 depending on the endian-ness. (must)
Head.mat - a 4x4 affine transformation matrix mapping from
voxel coordinates to real world coordinates. (must)
Head.pinfo - plane info for each plane of the volume.
Head.pinfo(1,:) - scale for each plane
Head.pinfo(2,:) - offset for each plane
The true voxel intensities of the jth image are given
by: val*Head.pinfo(1,j) + Head.pinfo(2,j)
Head.pinfo(3,:) - offset into image (in bytes).
If the size of pinfo is 3x1, then the volume is assumed
to be contiguous and each plane has the same scalefactor
and offset.
Head.private - a structure containing complete information in the
header
Header.Origin - the origin of the image;
-----------------------------------------------------------
Copyright(c) 2008~2010
State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
Written by YAN Chao-Gan
http://resting-fmri.sourceforge.net
Mail to Authors: <a href="Dawnwei.Song@gmail.com">Xiaowei Song</a>; <a href="ycg.yan@gmail.com">Chaogan Yan</a>
Version=1.3;
Release=20080420;
Revised by YAN Chao-Gan 080807: The NIFTI images would be saved in RPI coordination as the same as SPM5 usually did.
Last Revised by YAN Chao-Gan, 090420. rest_WriteAnalyzeImage.m only recognize 'float', thus change the parameter 'single' to 'float'.
-----------------------------------------------------------0001 function [] = rest_writefile(data,filename,isize,vsize,Header,dtype) 0002 %Write ANALYZE 7.5 or NIFTI file by YAN Chao-Gan 0003 % FORMAT function [] = rest_writefile(data,filename,isize,vsize,dtype) 0004 % data - data file. 0005 % filename - Analyze or NIFTI file (*.{hdr, img, nii}) 0006 % isize - the size of the data 0007 % vsize - the size of the voxel 0008 % dtype - the data type. 0009 % Header - It will decide to write ANALYZE7.5 or NIFTI file by 0010 % whether Header has the field 'mat'. 0011 % Analyze format - Header just has one subfield: Header.Origin - the origin of the images. 0012 % NIFTI format - Head.fname - the filename of the image. 0013 % Head.dim - the x, y and z dimensions of the volume 0014 % Head.dt - A 1x2 array. First element is datatype (see spm_type). 0015 % The second is 1 or 0 depending on the endian-ness. (must) 0016 % Head.mat - a 4x4 affine transformation matrix mapping from 0017 % voxel coordinates to real world coordinates. (must) 0018 % Head.pinfo - plane info for each plane of the volume. 0019 % Head.pinfo(1,:) - scale for each plane 0020 % Head.pinfo(2,:) - offset for each plane 0021 % The true voxel intensities of the jth image are given 0022 % by: val*Head.pinfo(1,j) + Head.pinfo(2,j) 0023 % Head.pinfo(3,:) - offset into image (in bytes). 0024 % If the size of pinfo is 3x1, then the volume is assumed 0025 % to be contiguous and each plane has the same scalefactor 0026 % and offset. 0027 % Head.private - a structure containing complete information in the 0028 % header 0029 % Header.Origin - the origin of the image; 0030 %----------------------------------------------------------- 0031 % Copyright(c) 2008~2010 0032 % State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University 0033 % Written by YAN Chao-Gan 0034 % http://resting-fmri.sourceforge.net 0035 % Mail to Authors: <a href="Dawnwei.Song@gmail.com">Xiaowei Song</a>; <a href="ycg.yan@gmail.com">Chaogan Yan</a> 0036 % Version=1.3; 0037 % Release=20080420; 0038 % Revised by YAN Chao-Gan 080807: The NIFTI images would be saved in RPI coordination as the same as SPM5 usually did. 0039 % Last Revised by YAN Chao-Gan, 090420. rest_WriteAnalyzeImage.m only recognize 'float', thus change the parameter 'single' to 'float'. 0040 %----------------------------------------------------------- 0041 0042 if isfield(Header,'mat') 0043 switch lower(dtype) 0044 case 'uint32' 0045 datatype = 768; 0046 case 'uint16' 0047 datatype = 512; 0048 case 'int8' 0049 datatype = 256; 0050 case {'float64','double'} 0051 datatype = 64; 0052 case {'float32','single'} 0053 datatype = 16; 0054 case 'int32' 0055 datatype = 8; 0056 case 'int16' 0057 datatype = 4; 0058 case 'uint8' 0059 datatype = 2; 0060 otherwise % need to add other decription 0061 error('unsupported data format now.'); 0062 end 0063 if Header.mat(1,1)>0 %The NIFTI images would be saved in RPI coordination as the same as SPM5 usually did. YAN Chao-Gan 080807 % <0 % I'd like to save the file in LPI coordination. Chaogan Yan 080610 0064 data = flipdim(data,1); 0065 Header.mat(1,:) = -1*Header.mat(1,:); 0066 end 0067 if Header.mat(2,2)<0 0068 data = flipdim(data,2); 0069 Header.mat(2,:) = -1*Header.mat(2,:); 0070 end 0071 if Header.mat(3,3)<0 0072 data = flipdim(data,3); 0073 Header.mat(3,:) = -1*Header.mat(3,:); 0074 end 0075 Header.dt =[datatype,0]; 0076 Header.vox =vsize; 0077 Header.dim =isize; 0078 Header.pinfo = [1;0;0]; 0079 rest_WriteNiftiImage(data,Header,filename); 0080 else 0081 if (dtype=='single') 0082 dtype='float'; %Revised by YAN Chao-Gan, 090420. rest_WriteAnalyzeImage.m only recognize 'float', thus change the parameter 'single' to 'float'. 0083 end 0084 rest_WriteAnalyzeImage(data,filename,isize,vsize,Header.Origin,dtype); 0085 end 0086 0087