主要流程：Realignment、Slice Timing Correction、Coregistration、Segmentation、Normalization
程式碼地址：https://github.com/zhoushusheng/fMRI_preprocessing/blob/main/stupid_batch_nii_third_formal_compilable.m
引數設定參考：
1：上海外國網課https://www.bilibili.com/video/BV1ye4y1m72P/spm_id_from=333.880.my_history.page.click&vd_source=9b75cfd2936571e6bc329144e79be03e
2：Andy's brain book：https://andysbrainbook.readthedocs.io/en/latest/SPM/SPM_Short_Course/SPM_04_Preprocessing.html
%-----------------------------------------------------------------------
% Job saved on 02-Sep-2019 18:21:16 by cfg_util (rev $Rev: 6942 $)
% spm SPM - SPM12 (7219)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%
% 這個m檔案用來執行spm的matlabbatch
% 該檔案中的檔案位置是基於linux系統的，如果是windows系統需要修改/為\
clear
% spm_path = '~\spm12'; %設定spm12的位置（這裡填的是安裝=spm12的絕對位置） 我這裡已經安裝好了
% addpath(spm_path);
spm('defaults', 'fmri');
spm_jobman('initcfg');
%%
subjectsdir = {'B:\fMRI\preprocess_for_batch\CN\'};% 這裡是data資料夾的絕對位置
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'}; % 單個或多個被試的資料夾
funcdir = fullfile('fMRI'); % 第一個Session的資料夾（由於preprocessing.mat中只新增了一個Session，所以這裡也只使用一個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'); % 第二個Session的資料夾
anatdir = fullfile('MRI'); % 結構像的資料夾
%%
% 設定基本的引數，在這裡設定方便後期修改
% head = spm_vol(sessionfiles{1});
% dimension = head.dim;
% slice_number = dimension(1,3);
% slice_number = 35;
% TR = 3;
% TA = TR-TR\slice_number;
% slice_order = [1:2:slice_number 2:2:slice_number];
% refslice1 = 35;
% voxel_size= [3.75 3.75 4];
% smoothing_kernel = [6 6 6];
%%
%每一個被試都建立一個工作流程
nsubj = length(subjects); % 被試的數量
jobs = cell(nsubj,1); % job的數量，每個被試一個job
nrun=1; % session的數量
%ntimepoint=190; %刪除了前面的10個時間點後剩餘的時間點
%%
for csubj = 24:36
subjdir = {spm_select('CPath',subjects{csubj}, subjectsdir)};%Cpath 的c = canonical
% 結構像資料夾
adir = spm_select('CPath', anatdir, subjdir); %選擇當前被試（csubj）的結構像資料夾
anatfile = strcat(spm_select('FPList', adir, '\\*.nii'),',1'); %在這個資料夾中.nii結尾的檔案，即結構像檔案 % As above, but return files with full paths (i.e. prefixes 'direc' to each)
%如果沒有結構像檔案就報錯
if isequal(anatfile, '')
warning(sprintf('No anat file found for %s', ...
subjects{csubj}))
return
end
% Session1資料夾
fdir = {spm_select('CPath', funcdir, subjdir)}; %選擇當前被試（csubj）的Session1資料夾
ffiles = spm_select('List', fdir, '\\*.nii'); %選擇這個資料夾中所有.nii結尾的檔案，即Session1的所有原始功能像檔案
%如果沒有功能像檔案就報錯
nimage = size(ffiles,1);
if nimage == 0
warning(sprintf('No functional file found for %s', subjects{csubj}))
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}); % 在這裡在每一個功能像檔案的絕對路徑後面新增,1
end
funcfiles{1,i} = {sessionfiles{i,:}}'; % 如果有多個Sessions，funcfiles中就會有多個sessionfiles
end
clear matlabbatch
length(cffiles);
head = spm_vol(sessionfiles{1});
dimension = head.dim;
descrip = head.descrip;
slice_number = dimension(1,3);
descrip={descrip};%char To cell
TR = regexp(descrip,'(?<=TR=)\d+|(?<=TR=)\d+\.\d+','match','once');
TR = str2double(TR);
TR = TR / 1000;
%如果沒有查到TR就報錯
if isequal(TR, '')
warning(sprintf('No TR parameter found for %s', ...
subjects{csubj}))
return
end
TA = TR-TR/slice_number;
%這個就得自己看了
% slice_order = [1:2:slice_number 2:2:slice_number];
% slice_order = [slice_number:-1:1];
slice_order = [slice_number:-1:1];
% preprocessing job
display 'Creating preprocessing job' %在matlab的命令列視窗顯示Creating preprocessing job
matlabbatch{1}.spm.spatial.realign.estwrite.data = {funcfiles{1,1}(:,1)};%這裡不加1 也行 ，就是上面查詢的時候
%%
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.sep = 4;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.interp = 2;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.weight = '';
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [2 1];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.interp = 4;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.mask = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.prefix = 'r';
matlabbatch{2}.spm.temporal.st.scans{1}(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));
matlabbatch{2}.spm.temporal.st.nslices = slice_number;
matlabbatch{2}.spm.temporal.st.tr = TR;
matlabbatch{2}.spm.temporal.st.ta = TA;
matlabbatch{2}.spm.temporal.st.so = slice_order;
matlabbatch{2}.spm.temporal.st.refslice = slice_number/2;
matlabbatch{2}.spm.temporal.st.prefix = 'a';
matlabbatch{3}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
matlabbatch{3}.spm.spatial.coreg.estimate.source = {anatfile};%ananfile 字串末尾得加一個1，細看對比stupid_batch_nii_third_formal_compilable
matlabbatch{3}.spm.spatial.coreg.estimate.other = {''};
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
matlabbatch{3}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
matlabbatch{4}.spm.spatial.preproc.channel.vols(1) = cfg_dep('Coregister: Estimate: Coregistered Images', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','cfiles'));
matlabbatch{4}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{4}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{4}.spm.spatial.preproc.channel.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.tissue(1).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,1'};
matlabbatch{4}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,2'};
matlabbatch{4}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{4}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,3'};
matlabbatch{4}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,4'};
matlabbatch{4}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{4}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,5'};
matlabbatch{4}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{4}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{4}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).tpm = {'C:\Program Files\MATLAB\R2021b\toolbox\spm12\tpm\TPM.nii,6'};
matlabbatch{4}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{4}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{4}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{4}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{4}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{4}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{4}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{4}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{4}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{4}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{4}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{4}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
matlabbatch{5}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));
matlabbatch{5}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Resliced Images (Sess 1)', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rfiles'));
matlabbatch{5}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70
78 76 85];
matlabbatch{5}.spm.spatial.normalise.write.woptions.vox = [2 2 2];
matlabbatch{5}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{5}.spm.spatial.normalise.write.woptions.prefix = 'w';
matlabbatch{6}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
matlabbatch{6}.spm.spatial.smooth.fwhm = [8 8 8];
matlabbatch{6}.spm.spatial.smooth.dtype = 0;
matlabbatch{6}.spm.spatial.smooth.im = 0;
matlabbatch{6}.spm.spatial.smooth.prefix = 's';
% 儲存matlabbatch
matfile = sprintf('preprocess_nii_%s.mat', subjects{csubj});
% save(matfile,'matlabbatch');
jobs{csubj} = matfile; %jobs這個變數中儲存了所有被試的matlabbatch
['Start preprocessing job' num2str(csubj)]
spm_jobman('run', matlabbatch);
end
%%
% 執行預處理的工作
% for csubj = 15:20
% display 'Start preprocessing job' %在matlab的命令列視窗顯示Start preprocessing job
% load(jobs{csubj});
% spm_jobman('run', matlabbatch);
% end