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RunPreproc.m
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RunPreproc.m
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%-----------------------------------------------------------------------
% SPM批处理脚本
%预处理
% spm SPM - SPM12 (7771)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%%清屏&清空工作区变量
clc
clear
spm fmri
%SPM路径
SPMPath = 'D:\spm12\spm12';
%%数据路径
datadir = 'G:\processing';
%%被试编号
subjects = [008 009 010 011 012 013 014];
%需要处理的run
RunList = {'run1' 'run2' 'run3' 'run4' 'run5' 'run6' 'run7' 'run8'};
%%建立循环
for ID = subjects
ID = num2str(ID, '%03d');
%结构像路径
anatPath = char(strcat(datadir, '\sub-', ID, '\anat'));
%读取结构像
T1w = cellstr(spm_select('ExtFPListRec', anatPath, '^?_.*\.nii'));
%功能像路径
funcPath = char(strcat(datadir, '\sub-', ID, '\func'));
%%%%时间层校正
clear matlabbatch;
for nrun = 1:length(RunList)
nrun = num2str(nrun);
matlabbatch{1}.spm.temporal.st.scans = {cellstr(spm_select('ExtFPListRec', [funcPath '\run' nrun '\'], 'run.*nii'))}';
matlabbatch{1}.spm.temporal.st.nslices = 40; %扫描层数
matlabbatch{1}.spm.temporal.st.tr = 2; %TR
matlabbatch{1}.spm.temporal.st.ta = 1.95; %TA
matlabbatch{1}.spm.temporal.st.so = [1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40]; %扫描顺序
matlabbatch{1}.spm.temporal.st.refslice = 2; %参考层
matlabbatch{1}.spm.temporal.st.prefix = 'a';
spm_jobman('run', matlabbatch);
end
%%%%头动校正
clear matlabbatch;
for nrun = 1:length(RunList)
nrun = num2str(nrun);
matlabbatch{1}.spm.spatial.realign.estwrite.data = {cellstr(spm_select('ExtFPListRec', [funcPath '\run' nrun '\'], 'a.*nii'))}'; %经过时间层校正的图像
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';
spm_jobman('run', matlabbatch);
end
%结构像与功能像对准
clear matlabbatch;
for nrun = 1:length(RunList)
nrun = num2str(nrun);
matlabbatch{1}.spm.spatial.coreg.estwrite.ref = cellstr(spm_select('ExtFPListRec', [funcPath '\run' nrun '\'], 'mean.*nii'))'; %头动校正的平均图像
matlabbatch{1}.spm.spatial.coreg.estwrite.source = T1w;
matlabbatch{1}.spm.spatial.coreg.estwrite.other = {''};
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.cost_fun = 'nmi';
matlabbatch{1}.spm.spatial.coreg.estwrite.eoptions.sep = [4 2];
matlabbatch{1}.spm.spatial.coreg.estwrite.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{1}.spm.spatial.coreg.estwrite.eoptions.fwhm = [7 7];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.interp = 4;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.mask = 0;
matlabbatch{1}.spm.spatial.coreg.estwrite.roptions.prefix = 'r';
spm_jobman('run', matlabbatch);
end
%组织分割
clear matlabbatch;
matlabbatch{1}.spm.spatial.preproc.channel.vols = cellstr(spm_select('ExtFPListRec', [anatPath], 'r.*nii'))'; %对齐过的结构像
matlabbatch{1}.spm.spatial.preproc.channel.biasreg = 0.001;
matlabbatch{1}.spm.spatial.preproc.channel.biasfwhm = 60;
matlabbatch{1}.spm.spatial.preproc.channel.write = [0 1];
matlabbatch{1}.spm.spatial.preproc.tissue(1).tpm = {[SPMPath '\tpm\TPM.nii,1']};
matlabbatch{1}.spm.spatial.preproc.tissue(1).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(1).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(1).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).tpm = {[SPMPath '\tpm\TPM.nii,2']};
matlabbatch{1}.spm.spatial.preproc.tissue(2).ngaus = 1;
matlabbatch{1}.spm.spatial.preproc.tissue(2).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(2).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).tpm = {[SPMPath '\tpm\TPM.nii,3']};
matlabbatch{1}.spm.spatial.preproc.tissue(3).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(3).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(3).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).tpm = {[SPMPath '\tpm\TPM.nii,4']};
matlabbatch{1}.spm.spatial.preproc.tissue(4).ngaus = 3;
matlabbatch{1}.spm.spatial.preproc.tissue(4).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(4).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).tpm = {[SPMPath '\tpm\TPM.nii,5']};
matlabbatch{1}.spm.spatial.preproc.tissue(5).ngaus = 4;
matlabbatch{1}.spm.spatial.preproc.tissue(5).native = [1 0];
matlabbatch{1}.spm.spatial.preproc.tissue(5).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).tpm = {[SPMPath '\tpm\TPM.nii,6']};
matlabbatch{1}.spm.spatial.preproc.tissue(6).ngaus = 2;
matlabbatch{1}.spm.spatial.preproc.tissue(6).native = [0 0];
matlabbatch{1}.spm.spatial.preproc.tissue(6).warped = [0 0];
matlabbatch{1}.spm.spatial.preproc.warp.mrf = 1;
matlabbatch{1}.spm.spatial.preproc.warp.cleanup = 1;
matlabbatch{1}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];
matlabbatch{1}.spm.spatial.preproc.warp.affreg = 'mni';
matlabbatch{1}.spm.spatial.preproc.warp.fwhm = 0;
matlabbatch{1}.spm.spatial.preproc.warp.samp = 3;
matlabbatch{1}.spm.spatial.preproc.warp.write = [0 1];
matlabbatch{1}.spm.spatial.preproc.warp.vox = NaN;
matlabbatch{1}.spm.spatial.preproc.warp.bb = [NaN NaN NaN
NaN NaN NaN];
spm_jobman('run', matlabbatch);
%配准到MNI152
clear matlabbatch;
for nrun = 1:length(RunList)
nrun = num2str(nrun);
DeformF = spm_select('list', [anatPath], 'y.*nii'); %形变场图，结构像文件夹下y开头的.nii文件
matlabbatch{1}.spm.spatial.normalise.write.subj.def = {strcat([anatPath], '\', DeformF)}';
data_r = []; %定义一个空矩阵用来装所有的功能像
rList = spm_select('ExtFPListRec', [funcPath '\run' nrun '\'], 'ra.*nii'); %经过头动校正的功能像
rListS = cellstr(rList);
data_r = [data_r;rListS]; %将所有功能像粘成一列
rList = []; rListS = []; %清除此两个变量的值，为下一循环准备
matlabbatch{1}.spm.spatial.normalise.write.subj.resample = data_r;
matlabbatch{1}.spm.spatial.normalise.write.woptions.bb = [-90 -126 -72
90 90 108];
matlabbatch{1}.spm.spatial.normalise.write.woptions.vox = [3 3 3];
matlabbatch{1}.spm.spatial.normalise.write.woptions.interp = 4;
matlabbatch{1}.spm.spatial.normalise.write.woptions.prefix = 'w';
spm_jobman('run', matlabbatch);
end
%空间平滑
clear matlabbatch;
for nrun = 1:length(RunList)
nrun = num2str(nrun);
data_w = []; %定义一个空矩阵用来装所有的功能像
wList = spm_select('ExtFPListRec', [funcPath '\run' nrun '\'], 'wra.*nii'); %经过标准化的功能像
wListS = cellstr(wList);
data_w = [data_w;wListS]; %将所有功能像粘成一列
wList = []; wListS = []; %清除此两个变量的值，为下一循环准备
matlabbatch{1}.spm.spatial.smooth.data = data_w;
matlabbatch{1}.spm.spatial.smooth.fwhm = [6 6 6];
matlabbatch{1}.spm.spatial.smooth.dtype = 0;
matlabbatch{1}.spm.spatial.smooth.im = 0;
matlabbatch{1}.spm.spatial.smooth.prefix = 's';
spm_jobman('run', matlabbatch);
end
end