Read file(ANALYZE 7.5, NIFTI, ...) for REST by YAN Chao-Gan
FORMAT function [Outdata,voxdim, Origin] = rest_readfile(filename)
filename - Analyze file (*.{hdr, img, nii})
Outdata - data file.
VoxDim - the size of the voxel.
Header - It's decided by the format of data file:
for ANALYZE 7.5 - Header.Origin - the origin of the image;
for NIFTI - 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.
Head.mat - a 4x4 affine transformation matrix mapping from
voxel coordinates to real world coordinates.
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;
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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=1.2;
Release=20080926;
Last Revised by YAN Chao-Gan 080926, fixed the bug when process ANALYZE format data.
-----------------------------------------------------------0001 function [Outdata,VoxDim,Header]=rest_readfile(imageIN,volumeIndex) 0002 % Read file(ANALYZE 7.5, NIFTI, ...) for REST by YAN Chao-Gan 0003 % FORMAT function [Outdata,voxdim, Origin] = rest_readfile(filename) 0004 % filename - Analyze file (*.{hdr, img, nii}) 0005 % Outdata - data file. 0006 % VoxDim - the size of the voxel. 0007 % Header - It's decided by the format of data file: 0008 % for ANALYZE 7.5 - Header.Origin - the origin of the image; 0009 % for NIFTI - Head.fname - the filename of the image. 0010 % Head.dim - the x, y and z dimensions of the volume 0011 % Head.dt - A 1x2 array. First element is datatype (see spm_type). 0012 % The second is 1 or 0 depending on the endian-ness. 0013 % Head.mat - a 4x4 affine transformation matrix mapping from 0014 % voxel coordinates to real world coordinates. 0015 % Head.pinfo - plane info for each plane of the volume. 0016 % Head.pinfo(1,:) - scale for each plane 0017 % Head.pinfo(2,:) - offset for each plane 0018 % The true voxel intensities of the jth image are given 0019 % by: val*Head.pinfo(1,j) + Head.pinfo(2,j) 0020 % Head.pinfo(3,:) - offset into image (in bytes). 0021 % If the size of pinfo is 3x1, then the volume is assumed 0022 % to be contiguous and each plane has the same scalefactor 0023 % and offset. 0024 % Head.private - a structure containing complete information in the 0025 % header 0026 % Header.Origin - the origin of the image; 0027 %----------------------------------------------------------- 0028 % Copyright(c) 2008~2010 0029 % State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University 0030 % Written by YAN Chao-Gan 0031 % http://resting-fmri.sourceforge.net 0032 % Mail to Authors: <a href="Dawnwei.Song@gmail.com">Xiaowei Song</a>; <a href="ycg.yan@gmail.com">Chaogan Yan</a> 0033 % Version=1.2; 0034 % Release=20080926; 0035 % Last Revised by YAN Chao-Gan 080926, fixed the bug when process ANALYZE format data. 0036 %----------------------------------------------------------- 0037 if ~exist('volumeIndex', 'var') 0038 volumeIndex=1; 0039 end 0040 0041 if ~(strcmpi(imageIN(end-3:end), '.hdr') || strcmpi(imageIN(end-3:end), '.img') || strcmpi(imageIN(end-3:end), '.nii')) 0042 imageIN = [imageIN,'.img']; 0043 end 0044 0045 [pth,nam,ext] = fileparts(imageIN); 0046 switch ext 0047 case {'.img','.hdr'} 0048 hname = fullfile(pth,[nam '.hdr']); 0049 case {'.nii'} 0050 hname = fullfile(pth,[nam '.nii']); 0051 otherwise 0052 hname = fullfile(pth,[nam '.hdr']); 0053 end; 0054 fp = fopen(hname,'r','native'); 0055 if(fp>0) 0056 fseek(fp,344,'bof'); 0057 mgc = deblank(char(fread(fp,4,'uint8')')); 0058 fclose(fp); %YAN Chao-Gan 080926, fixed the bug when process ANALYZE format data. 0059 switch mgc 0060 case {'ni1','n+1'} 0061 [Outdata,Header]= rest_ReadNiftiImage(imageIN,volumeIndex); 0062 if Header.mat(1,1)>0 % Because the Song's former edition use the radiology convention, So I treat all the Img and Head in RPI coordination. Chaogan Yan 080610 0063 Outdata = flipdim(Outdata,1); 0064 Header.mat(1,:) = -1*Header.mat(1,:); 0065 end 0066 if Header.mat(2,2)<0 0067 Outdata = flipdim(Outdata,2); 0068 Header.mat(2,:) = -1*Header.mat(2,:); 0069 end 0070 if Header.mat(3,3)<0 0071 Outdata = flipdim(Outdata,3); 0072 Header.mat(3,:) = -1*Header.mat(3,:); 0073 end 0074 temp=inv(Header.mat)*[0,0,0,1]'; 0075 Header.Origin=temp(1:3)'; 0076 VoxDim=abs([Header.mat(1,1),Header.mat(2,2),Header.mat(3,3)]); 0077 otherwise 0078 [Outdata,VoxDim,Origin]= rest_ReadAnalyzeImage(imageIN); 0079 Header.Origin=Origin; 0080 end; 0081 else 0082 error(sprintf('Error opening header file. Please check whether the %s file exist.',hname)); 0083 fclose(fp); %YAN Chao-Gan 080926, fixed the bug when process ANALYZE format data. 0084 end 0085 %fclose(fp); %YAN Chao-Gan 080926, fixed the bug when process ANALYZE format data.