Write file(NIFTI, ...) for REST by CHEN Gui-Wen and YAN Chao-Gan
%------------------------------------------------------------------------
Write data (Data) with a specified header (Head) into a image file with format
of Nifti 1.1. The data (Data) should be 3D matrix, the header (Head) should
be a structure the same as SPM5. If the filename (imageOUT) is with
extra name as '.img', then it will generate two files (header and
data seperately), or else, '.nii', it will generate single file with header
and data together.
Usage: [flag] = rest_WriteNiftiImage(Data,Head,imageOUT)
Input:
1. Data - Data of 3D matrix to write
2. Head - a structure containing image volume information, the structure
is the same with a structure have read
The elements in the structure are:
Head.fname - the filename of the image. If the filename is not set,
just use the parameter.
Head.vox - A 1x3 array. It is the size of a voxel. (Must)
Head.origin - A 1x3 array. It is the origin of coordinate. (Must)
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.
The scale and intercept will be changed according to the
data to write
3. imageOUT - the path and filename of image file to output [path\*.img or *.nii]
Output:
1. flag - a flag for all done, 1: successful, 0: fail
%------------------------------------------------------------------------
Copyright (C) 2007 Neuroimage Computing Group, State Key Laboratory of
Cognitive Neuroscience and Learning
Guiwen Chen, gwenchill@gmail.com
@(#)rest_WriteNiftiImage.m ver 2.0, 07/11/21
%------------------------------------------------------------------------
Revised by YAN Chao-Gan 080621
ycg.yan@gmail.com0001 function [flag] = rest_WriteNiftiImage(Data,Head,imageOUT) 0002 % Write file(NIFTI, ...) for REST by CHEN Gui-Wen and YAN Chao-Gan 0003 % %------------------------------------------------------------------------ 0004 % Write data (Data) with a specified header (Head) into a image file with format 0005 % of Nifti 1.1. The data (Data) should be 3D matrix, the header (Head) should 0006 % be a structure the same as SPM5. If the filename (imageOUT) is with 0007 % extra name as '.img', then it will generate two files (header and 0008 % data seperately), or else, '.nii', it will generate single file with header 0009 % and data together. 0010 % 0011 % Usage: [flag] = rest_WriteNiftiImage(Data,Head,imageOUT) 0012 % 0013 % Input: 0014 % 1. Data - Data of 3D matrix to write 0015 % 2. Head - a structure containing image volume information, the structure 0016 % is the same with a structure have read 0017 % The elements in the structure are: 0018 % Head.fname - the filename of the image. If the filename is not set, 0019 % just use the parameter. 0020 % Head.vox - A 1x3 array. It is the size of a voxel. (Must) 0021 % Head.origin - A 1x3 array. It is the origin of coordinate. (Must) 0022 % Head.dim - the x, y and z dimensions of the volume 0023 % Head.dt - A 1x2 array. First element is datatype (see spm_type). 0024 % The second is 1 or 0 depending on the endian-ness. 0025 % Head.mat - a 4x4 affine transformation matrix mapping from 0026 % voxel coordinates to real world coordinates. 0027 % Head.pinfo - plane info for each plane of the volume. 0028 % Head.pinfo(1,:) - scale for each plane 0029 % Head.pinfo(2,:) - offset for each plane 0030 % The true voxel intensities of the jth image are given 0031 % by: val*Head.pinfo(1,j) + Head.pinfo(2,j) 0032 % Head.pinfo(3,:) - offset into image (in bytes). 0033 % If the size of pinfo is 3x1, then the volume is assumed 0034 % to be contiguous and each plane has the same scalefactor 0035 % and offset. 0036 % The scale and intercept will be changed according to the 0037 % data to write 0038 % 3. imageOUT - the path and filename of image file to output [path\*.img or *.nii] 0039 % Output: 0040 % 1. flag - a flag for all done, 1: successful, 0: fail 0041 % %------------------------------------------------------------------------ 0042 % Copyright (C) 2007 Neuroimage Computing Group, State Key Laboratory of 0043 % Cognitive Neuroscience and Learning 0044 % 0045 % Guiwen Chen, gwenchill@gmail.com 0046 % @(#)rest_WriteNiftiImage.m ver 2.0, 07/11/21 0047 % %------------------------------------------------------------------------ 0048 % Revised by YAN Chao-Gan 080621 0049 % ycg.yan@gmail.com 0050 0051 % get the SPM path to use 0052 FilePath = which('rest.m'); 0053 [giftPath, fileN, extn] = fileparts(FilePath); 0054 spmPath = fullfile(giftPath, 'rest_spm5_files'); 0055 oldDir = pwd; 0056 addpath(spmPath); 0057 0058 try 0059 % cd(spmPath); 0060 [pth,nam,ext] = fileparts(imageOUT); %%Added by YAN Chao-Gan 0061 if isempty(ext) 0062 imageOUT=[imageOUT,'.img']; 0063 end 0064 0065 0066 V=Head; 0067 0068 %construct the file name and path 0069 if(~exist('imageOUT','var')) 0070 if(~isfield(Head,'fname')), 0071 fName=Head.fname; 0072 end 0073 else 0074 fName=imageOUT; 0075 end 0076 %fName=imgPath; 0077 if isempty(fileparts(fName)) 0078 fName = fullfile(oldDir, fName); 0079 end 0080 V.fname=fName; 0081 0082 nic_spm_write_vol(V, Data); 0083 0084 clear V; 0085 flag=1;% Successful 0086 rmpath(spmPath); 0087 % cd(oldDir); 0088 catch 0089 rmpath(spmPath); 0090 flag=0;% fail 0091 % cd(oldDir); 0092 error('Meet error while writing the data'); 0093 end 0094