运行说明：subjectsdir换成自己的文件夹地址， 有多少个受试者的DICOM就有多少个subjects子元素 。
%-----------------------------------------------------------------------
% Job saved on 02-Sep-2019 18:21:16 by cfg_util (rev $Rev: 6942 $)
% spm SPM - SPM12 (7219)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
% 这个m文件用来运行spm的matlabbatch
% 该文件中的文件位置是基于linux系统的，如果是windows系统需要修改/为\
clear
% spm_path = '~\spm12'; %设置spm12的位置（这里填的是安装=spm12的绝对位置） 我这里已经安装好了
% addpath(spm_path);
spm('defaults', 'fmri');
spm_jobman('initcfg');
%%
subjectsdir = {'B:\fMRI\preprocess_for_batch\CN'};% 这里是data文件夹的绝对位置
subjects = {'sbj01','sbj02','sbj03','sbj04','sbj05','sbj06','sbj07','sbj08','sbj09','sbj10','sbj11','sbj12','sbj13','sbj14','sbj15','sbj16','sbj17','sbj18','sbj19','sbj20','sbj21','sbj22','sbj23','sbj24','sbj25','sbj26','sbj27','sbj28','sbj29','sbj30','sbj31','sbj32','sbj33','sbj34','sbj35','sbj36'}; % 单个或多个被试的文件夹
funcdir = fullfile('fMRI_DICOM'); % 第一个Session的文件夹（由于preprocessing.mat中只添加了一个Session，所以这里也只使用一个Session。）
% F = fullfile(FOLDERNAME1, FOLDERNAME2, ..., FILENAME) builds a full
% file specification F from the folders and file name specified. Input
% arguments FOLDERNAME1, FOLDERNAME2, etc. and FILENAME can be strings,
% character vectors, or cell arrays of character vectors. Non-scalar
% strings and cell arrays of character vectors must all be the same size.
% FULLFILE collapses inner repeated file separators unless they appear at
% the beginning of the full file specification. FULLFILE also collapses
% relative folders indicated by the dot symbol, unless they appear at
% the end of the full file specification. Relative folders indicated
% by the double-dot symbol are not collapsed.
%
% funcdir2 = fullfile('Session2'); % 第二个Session的文件夹
anatdir = fullfile('MRI_DICOM'); % 结构像的文件夹
nsubj = length(subjects); % 被试的数量
jobs_fMRI = cell(1,1); % job的数量，每个被试一个job
jobs_MRI = cell(1,1);
nsubj =2;
inputs = cell(0,1);
nrun=1; % session的数量
%ntimepoint=190; %删除了前面的10个时间点后剩余的时间点
%%
for csubj_fMRI = 1:36
subjdir = {spm_select('CPath',subjects{csubj_fMRI}, subjectsdir)};%Cpath 的c = canonical
% Session1文件夹
fdir = {spm_select('CPath', funcdir, subjdir)}; %选择当前被试（csubj_fMRI）的Session1文件夹
ffiles = spm_select('List', fdir, '\\*.dcm'); %选择这个文件夹中所有.nii结尾的文件，即Session1的所有原始功能像文件
%如果没有功能像文件就报错
nimage = size(ffiles,1);
if nimage == 0
warning(sprintf('No functional file found for %s', subjects{csubj_fMRI}))
return
end
cffiles = cellstr(ffiles);
ntimepoint = length(cffiles);
funcfiles = cell(1, nrun);
sessionfiles = cell(nrun,ntimepoint);
for i = 1:nrun
for j = 1:ntimepoint
sessionfiles{i,j}=strcat(fdir{1},'\',cffiles{j}); % 在这里在每一个功能像文件的绝对路径后面添加,1
end
funcfiles{1,i} = {sessionfiles{i,:}}'; % 如果有多个Sessions，funcfiles中就会有多个sessionfiles
end
clear matlabbatch
% preprocessing job
display 'Creating preprocessing job' %在matlab的命令行窗口显示Creating preprocessing job
goalDirectory = {'B:\fMRI\preprocess_for_batch\CN'};%这样生成的cell 没有'' ，没有显示内容的类型
goalDirectory_subj = {spm_select('CPath', subjects{csubj_fMRI} ,goalDirectory)};% 这样生成的也 没有
goalDirectory_subj = char(goalDirectory_subj);%这样生成的也没有'' 但是会显示类型
if ~exist(goalDirectory_subj, 'dir')
% mkdir goalDirectory subjects{csubj_fMRI}%这里十分可恶 goalDirectory 不能识别为变量
goalDirectory = goalDirectory{1};
% mkdir [goalDirectory] subjects{csubj_fMRI}
mkdir([goalDirectory '\' subjects{csubj_fMRI}]);%这就是真理 上matlab 网站找着了
%% else
% warning(sprintf('Folder has been created and make sure if files needed has exited', subjects{csubj_fMRI}))
% return
end
goalDirectory_subj = {goalDirectory_subj};%没有前面一行代码 这样显示的会有'' ，加上前面一行的话 会变成""
goalDirectory_subj_fMRI = {spm_select('CPath', 'fMRI' ,goalDirectory_subj)}; %这个会自动合并 connonical {'fMRI'} 把 {}去了
goalDirectory_subj_fMRI = char(goalDirectory_subj_fMRI);%为什么这里要加1在花括号里？为甚这样就行？可能因为前面的代码，生成的就是一个cell。那更前面不也是嘛，为什么就行？原因出来了在上一行。
if ~exist(goalDirectory_subj_fMRI, 'dir')%经过这里一手 就会把goalDirectory 变成cell下面就不能用了
%string = convertCharsToStrings(goalDirectory_subj_fMRI);
goalDirectory_subj = goalDirectory_subj{1};
% mkdir [goalDirectory] subjects{csubj_fMRI}
mkdir([goalDirectory_subj '\' 'fMRI']);%这就是真理 上matlab 网站找着了
else
warning(sprintf('Folder has been created and make sure if files needed has exited', subjects{csubj_fMRI}))
return
end
matlabbatch{1}.spm.util.import.dicom.data = funcfiles{1,1}(:,1);
matlabbatch{1}.spm.util.import.dicom.root = 'flat';
matlabbatch{1}.spm.util.import.dicom.outdir = {goalDirectory_subj_fMRI};
matlabbatch{1}.spm.util.import.dicom.protfilter = '.*';
matlabbatch{1}.spm.util.import.dicom.convopts.format = 'nii';
matlabbatch{1}.spm.util.import.dicom.convopts.meta = 0;
matlabbatch{1}.spm.util.import.dicom.convopts.icedims = 0;
matfile = sprintf('preprocess_fMRI_%s.mat', subjects{csubj_fMRI});
% save(matfile,'matlabbatch');
jobs_fMRI{csubj_fMRI} = matfile; %jobs这个变量中存储了所有被试的matlabbatch
spm_jobman('run',matlabbatch);
end
for csubj_MRI = 1:36
subjdir = {spm_select('CPath',subjects{csubj_MRI}, subjectsdir)};%Cpath 的c = canonical
% Session1文件夹
fdir = {spm_select('CPath', anatdir, subjdir)}; %选择当前被试（csubj_fMRI）的Session1文件夹
ffiles = spm_select('List', fdir, '\\*.dcm'); %选择这个文件夹中所有.nii结尾的文件，即Session1的所有原始功能像文件
%如果没有功能像文件就报错
nimage = size(ffiles,1);
if nimage == 0
warning(sprintf('No functional file found for %s', subjects{csubj_MRI}))
return
end
cffiles = cellstr(ffiles);
ntimepoint = length(cffiles);
funcfiles = cell(1, nrun);
sessionfiles = cell(nrun,ntimepoint);
for i = 1:nrun
for j = 1:ntimepoint
sessionfiles{i,j}=strcat(fdir{1},'\',cffiles{j}); % 在这里在每一个功能像文件的绝对路径后面添加,1
end
funcfiles{1,i} = {sessionfiles{i,:}}'; % 如果有多个Sessions，funcfiles中就会有多个sessionfiles
end
clear matlabbatch
% preprocessing job
display 'Creating preprocessing job' %在matlab的命令行窗口显示Creating preprocessing job
goalDirectory = {'B:\fMRI\preprocess_for_batch\CN'};
goalDirectory_subj = {spm_select('CPath', subjects{csubj_MRI} ,goalDirectory)};
goalDirectory_subj = char(goalDirectory_subj);
if ~exist(goalDirectory_subj, 'dir')
goalDirectory = goalDirectory{1};
mkdir([goalDirectory '\' subjects{csubj_MRI}]);
end
goalDirectory_subj = {goalDirectory_subj};
goalDirectory_MRI = {spm_select('CPath', 'MRI' ,goalDirectory_subj)};
goalDirectory_MRI = char(goalDirectory_MRI);
if ~exist(goalDirectory_MRI, 'dir')
% mkdir 'B:\fMRI\preprocess_for_batch\AD' MRI
goalDirectory_subj = goalDirectory_subj{1};
mkdir([goalDirectory_subj '\' 'MRI']);
else
warning(sprintf('Folder has been created and make sure if files needed has exited', subjects{csubj_MRI}))
return
end
matlabbatch{1}.spm.util.import.dicom.data = funcfiles{1,1}(:,1);
matlabbatch{1}.spm.util.import.dicom.root = 'flat';
matlabbatch{1}.spm.util.import.dicom.outdir = {goalDirectory_MRI};
matlabbatch{1}.spm.util.import.dicom.protfilter = '.*';
matlabbatch{1}.spm.util.import.dicom.convopts.format = 'nii';
matlabbatch{1}.spm.util.import.dicom.convopts.meta = 0;
matlabbatch{1}.spm.util.import.dicom.convopts.icedims = 0;
matfile = sprintf('preprocess_MRI_%s.mat', subjects{csubj_MRI});
% save(matfile,'matlabbatch');
jobs_MRI{csubj_MRI} = matfile; %jobs这个变量中存储了所有被试的matlabbatch
spm_jobman('run',matlabbatch);
end
标签：fMRI,NII,DICOM,matlabbatch,spm,csubj,格式,goalDirectory,subj From： https://www.cnblogs.com/zhoushusheng/p/18321667