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fMRI_1st_level.m
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fMRI_1st_level.m
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function fMRI_1st_level(subject_root_dir, anatomical_nii, mean_functional_nii, filePrefix)
% expects prefix rar
matlabbatch{1}.spm.stats.fmri_spec.dir = {'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\stats'};
matlabbatch{1}.spm.stats.fmri_spec.timing.units = 'scans';
matlabbatch{1}.spm.stats.fmri_spec.timing.RT = 3;
matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t = 16;
matlabbatch{1}.spm.stats.fmri_spec.timing.fmri_t0 = 8;
%%
matlabbatch{1}.spm.stats.fmri_spec.sess.scans = {
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_001.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_002.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_003.nii,1'
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'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_129.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_130.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_131.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_132.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_133.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_134.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_135.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_136.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_137.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_138.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_139.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_140.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_141.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_142.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_143.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_144.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_145.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_146.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_147.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_148.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_149.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_150.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_151.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_152.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_153.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_154.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_155.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_156.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_157.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_158.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_159.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_160.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_161.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_162.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_163.nii,1'
'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\wrar20120505_194300s006a1001_164.nii,1'
};
%%
matlabbatch{1}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});
matlabbatch{1}.spm.stats.fmri_spec.sess.multi = {'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\onsets.mat'};
matlabbatch{1}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});
matlabbatch{1}.spm.stats.fmri_spec.sess.multi_reg = {'G:\My Drive\Msc neuroscience\1st year 2021\fMRI lab course\Lesson_06_data\data\550_preprocessed\rp_20120505_194300s006a1001_001.txt'};
matlabbatch{1}.spm.stats.fmri_spec.sess.hpf = 128;
matlabbatch{1}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});
matlabbatch{1}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];
matlabbatch{1}.spm.stats.fmri_spec.volt = 1;
matlabbatch{1}.spm.stats.fmri_spec.global = 'None';
matlabbatch{1}.spm.stats.fmri_spec.mthresh = 0.8;
matlabbatch{1}.spm.stats.fmri_spec.mask = {''};
matlabbatch{1}.spm.stats.fmri_spec.cvi = 'AR(1)';
spm_jobman('run' , matlabbatch);
matlabbatch = [];