%-----------------------------------------------------------------------
% Job saved on 12-Apr-2024 20:58:03 by cfg_util (rev $Rev: 6942 $)
% spm SPM - SPM12 (7219)
% cfg_basicio BasicIO - Unknown
%-----------------------------------------------------------------------
%% init spm
spm('defaults', 'fmri')
spm_jobman('initcfg')

data_rootdir = '/Data/'
subjlist = dir(data_rootdir)
for subjidx = 3:length(subjlist)
    subj = subjlist(subjidx).name
    matlabbatch = PreprocAndFirstlevel(subj, data_rootdir);
    spm_jobman('run', matlabbatch)
end

    
    
% 1st level analysis
function matlabbatch = PreprocAndFirstlevel(subj, data_rootdir)
    matlabbatch{1}.cfg_basicio.file_dir.file_ops.cfg_named_file.name = 'first_level';
    matlabbatch{1}.cfg_basicio.file_dir.file_ops.cfg_named_file.files = {
                                                                         {[data_rootdir subj '/task.nii']}
                                                                         {[data_rootdir subj '/t1.nii']}
                                                                         }';
    matlabbatch{2}.cfg_basicio.file_dir.dir_ops.cfg_named_dir.name = 'first_level';
    matlabbatch{2}.cfg_basicio.file_dir.dir_ops.cfg_named_dir.dirs = {{[data_rootdir subj '/first_level']}};
    matlabbatch{3}.spm.temporal.st.scans{1}(1) = cfg_dep('Named File Selector: first_level(1) - Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files', '{}',{1}));
    matlabbatch{3}.spm.temporal.st.nslices = 33;
    matlabbatch{3}.spm.temporal.st.tr = 2;
    matlabbatch{3}.spm.temporal.st.ta = 0;
    matlabbatch{3}.spm.temporal.st.so = [0 1.03125 0.0625 1.09375 0.125 1.14844 0.1875 1.21094 0.24219 1.27344 0.30469 1.33594 0.36719 1.39062 0.42969 1.45312 0.48438 1.51562 0.54688 1.57812 0.60938 1.63281 0.67188 1.69531 0.72656 1.75781 0.78906 1.82031 0.85156 1.875 0.90625 1.9375 0.96875];
    matlabbatch{3}.spm.temporal.st.refslice = 33;
    matlabbatch{3}.spm.temporal.st.prefix = 'a';
    matlabbatch{4}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('Slice Timing: Slice Timing Corr. Images (Sess 1)', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.sep = 4;
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.rtm = 0;
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.interp = 2;
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
    matlabbatch{4}.spm.spatial.realign.estwrite.eoptions.weight = '';
    matlabbatch{4}.spm.spatial.realign.estwrite.roptions.which = [2 1];
    matlabbatch{4}.spm.spatial.realign.estwrite.roptions.interp = 4;
    matlabbatch{4}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
    matlabbatch{4}.spm.spatial.realign.estwrite.roptions.mask = 1;
    matlabbatch{4}.spm.spatial.realign.estwrite.roptions.prefix = 'r';
    matlabbatch{5}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Named File Selector: first_level(2) - Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files', '{}',{2}));
    matlabbatch{5}.spm.spatial.coreg.estimate.source(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));
    matlabbatch{5}.spm.spatial.coreg.estimate.other = {''};
    matlabbatch{5}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';
    matlabbatch{5}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];
    matlabbatch{5}.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{5}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];
    matlabbatch{6}.spm.spatial.normalise.estwrite.subj.vol(1) = cfg_dep('Named File Selector: first_level(2) - Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files', '{}',{2}));
    matlabbatch{6}.spm.spatial.normalise.estwrite.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Resliced Images (Sess 1)', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rfiles'));
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.biasreg = 0.0001;
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.biasfwhm = 60;
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.tpm = {'/home/matlab/spm12/tpm/TPM.nii'};
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.affreg = 'mni';
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.reg = [0 0.001 0.5 0.05 0.2];
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.fwhm = 0;
    matlabbatch{6}.spm.spatial.normalise.estwrite.eoptions.samp = 3;
    matlabbatch{6}.spm.spatial.normalise.estwrite.woptions.bb = [-78 -112 -70
                                                                 78 76 85];
    matlabbatch{6}.spm.spatial.normalise.estwrite.woptions.vox = [2 2 2];
    matlabbatch{6}.spm.spatial.normalise.estwrite.woptions.interp = 4;
    matlabbatch{6}.spm.spatial.normalise.estwrite.woptions.prefix = 'w';
    matlabbatch{7}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Estimate & Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{6}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));
    matlabbatch{7}.spm.spatial.smooth.fwhm = [4 4 4];
    matlabbatch{7}.spm.spatial.smooth.dtype = 0;
    matlabbatch{7}.spm.spatial.smooth.im = 0;
    matlabbatch{7}.spm.spatial.smooth.prefix = 's';
    matlabbatch{8}.spm.stats.fmri_spec.dir(1) = cfg_dep('Named Directory Selector: first_level(1)', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','dirs', '{}',{1}));
    matlabbatch{8}.spm.stats.fmri_spec.timing.units = 'secs';
    matlabbatch{8}.spm.stats.fmri_spec.timing.RT = 2;
    matlabbatch{8}.spm.stats.fmri_spec.timing.fmri_t = 16;
    matlabbatch{8}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
    matlabbatch{8}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).name = 'dynamic';
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).onset = [28
                                                             50
                                                             94
                                                             116
                                                             182
                                                             226
                                                             270
                                                             314
                                                             358
                                                             402
                                                             446
                                                             512
                                                             534
                                                             600
                                                             644
                                                             666];
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).duration = 6;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).tmod = 0;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).pmod = struct('name', {}, 'param', {}, 'poly', {});
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(1).orth = 1;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).name = 'static';
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).onset = [4
                                                             70
                                                             136
                                                             158
                                                             202
                                                             246
                                                             290
                                                             334
                                                             378
                                                             422
                                                             466
                                                             488
                                                             554
                                                             576
                                                             620
                                                             686];
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).duration = 6;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).tmod = 0;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).pmod = struct('name', {}, 'param', {}, 'poly', {});
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(2).orth = 1;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).name = 'rest';
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).onset = [16
                                                                38
                                                                60
                                                                82
                                                                104
                                                                126
                                                                148
                                                                170
                                                                192
                                                                214
                                                                236
                                                                258
                                                                280
                                                                302
                                                                324
                                                                346
                                                                368
                                                                390
                                                                412
                                                                434
                                                                456
                                                                478
                                                                500
                                                                522
                                                                544
                                                                566
                                                                588
                                                                610
                                                                632
                                                                654
                                                                676
                                                                698];
    %%
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).duration = 8;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).tmod = 0;
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).pmod = struct('name', {}, 'param', {}, 'poly', {});
    matlabbatch{8}.spm.stats.fmri_spec.sess.cond(3).orth = 1;
    matlabbatch{8}.spm.stats.fmri_spec.sess.multi = {''};
    matlabbatch{8}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
    matlabbatch{8}.spm.stats.fmri_spec.sess.multi_reg(1) = cfg_dep('Realign: Estimate & Reslice: Realignment Param File (Sess 1)', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','rpfile'));
    matlabbatch{8}.spm.stats.fmri_spec.sess.hpf = 128;
    matlabbatch{8}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});
    matlabbatch{8}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];
    matlabbatch{8}.spm.stats.fmri_spec.volt = 1;
    matlabbatch{8}.spm.stats.fmri_spec.global = 'None';
    matlabbatch{8}.spm.stats.fmri_spec.mthresh = 0.8;
    matlabbatch{8}.spm.stats.fmri_spec.mask = {''};
    matlabbatch{8}.spm.stats.fmri_spec.cvi = 'AR(1)';
    matlabbatch{9}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
    matlabbatch{9}.spm.stats.fmri_est.write_residuals = 0;
    matlabbatch{9}.spm.stats.fmri_est.method.Classical = 1;
    matlabbatch{10}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{9}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
    matlabbatch{10}.spm.stats.con.consess{1}.tcon.name = 'dynamic_gt_static';
    matlabbatch{10}.spm.stats.con.consess{1}.tcon.weights = [1 -1 0 0 0 0 0 0 0];
    matlabbatch{10}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
    matlabbatch{10}.spm.stats.con.consess{2}.tcon.name = 'dynamic_lt_static';
    matlabbatch{10}.spm.stats.con.consess{2}.tcon.weights = [-1 1 0 0 0 0 0 0 0];
    matlabbatch{10}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
    matlabbatch{10}.spm.stats.con.consess{3}.tcon.name = 'dynamic_gt_rest';
    matlabbatch{10}.spm.stats.con.consess{3}.tcon.weights = [1 0 -1 0 0 0 0 0 0];
    matlabbatch{10}.spm.stats.con.consess{3}.tcon.sessrep = 'none';
    matlabbatch{10}.spm.stats.con.consess{4}.tcon.name = 'static_gt_rest';
    matlabbatch{10}.spm.stats.con.consess{4}.tcon.weights = [0 1 -1 0 0 0 0 0 0];
    matlabbatch{10}.spm.stats.con.consess{4}.tcon.sessrep = 'none';
    matlabbatch{10}.spm.stats.con.consess{5}.tcon.name = 'Comprehensive_gt_rest';
    matlabbatch{10}.spm.stats.con.consess{5}.tcon.weights = [1/2 1/2 -1 0 0 0 0 0 0];
    matlabbatch{10}.spm.stats.con.consess{5}.tcon.sessrep = 'none';
    matlabbatch{10}.spm.stats.con.delete = 0;
    matlabbatch{11}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
    matlabbatch{11}.spm.stats.results.conspec.titlestr = '';
    matlabbatch{11}.spm.stats.results.conspec.contrasts = Inf;
    matlabbatch{11}.spm.stats.results.conspec.threshdesc = 'FDR';
    matlabbatch{11}.spm.stats.results.conspec.thresh = 0.05;
    matlabbatch{11}.spm.stats.results.conspec.extent = 0;
    matlabbatch{11}.spm.stats.results.conspec.conjunction = 1;
    matlabbatch{11}.spm.stats.results.conspec.mask.none = 1;
    matlabbatch{11}.spm.stats.results.units = 1;
    matlabbatch{11}.spm.stats.results.export{1}.ps = true;
end