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pm8_STAT_PET.m
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function pm8_STAT_PET(smoothing)
% smoothing 0 = non; 1 = oui
% action : 1 = SPM sur images sans PET pvc; 2 = SPM sur images avec PET PVC; 3 = SnPM
%-----------------------------------------------------------------------
global data;
if ~nargin
fprintf(1,'Spécifiez le smoothing\n');
return
end
spm pet;
root_pth ='D:\thk';
addpath('D:\thk\thk_codes')
data = pm0_COF_data(fullfile(root_pth));
% =========================================================================
% Smooth MR files
% =========================================================================
if smoothing == 1
MRFiles = [];
for isub = 1:size(data,2)
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('SUV.+',data(isub).id,'.+\.nii')))
MRFiles = [MRFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('SUV.+',data(isub).id,'.+\.nii')))];
end
end
matlabbatch{1}.spm.spatial.smooth.data = MRFiles;
matlabbatch{1}.spm.spatial.smooth.fwhm = [8 8 8];
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);
clear matlabbatch
end
% SUV without PETPVC (SUVwrrns)
fprintf(1,'SUV without PETPVC\n')
PETFiles = [];
for isub = 1:size(data,2)-1
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVwrrns',data(isub).id,'.+60.nii')))
PETFiles = [PETFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVwrrns',data(isub).id,'.+60.nii')))];
end
end
matlabbatch{1}.spm.stats.factorial_design.dir = {'d:\thk\RES_SUV_woPVC'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans1 = {'d:\thk\COF999\PET\sSUVwrrnsCOF999_b47_2d88_de10_01010001_40-60.nii,1'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans2 = PETFiles;
matlabbatch{1}.spm.stats.factorial_design.des.t2.dept = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.variance = 1;
matlabbatch{1}.spm.stats.factorial_design.des.t2.gmsca = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.ancova = 0;
matlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.im = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.em = {'D:\thk\thk_codes\mask_20180209.nii'};
matlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;
matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'P>T';
matlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = [1 -1];
matlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.name = 'P<T';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.weights = [-1 1];
matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 0;
spm_jobman('run',matlabbatch);
clear matlabbatch
% SUV with PETPVC
fprintf(1,'SUV with PETPVC\n')
PETFiles = [];
for isub = 1:size(data,2)
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVwPrrns',data(isub).id,'.+\.nii')))
PETFiles = [PETFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVwPrrns',data(isub).id,'.+\.nii')))];
end
end
matlabbatch{1}.spm.stats.factorial_design.dir = {'d:\thk\RES_SUV_wPVC'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans1 = {'d:\thk\COF999\PET\sSUVwPrrnsCOF999_b47_2d88_de10_01010001_40-60.nii,1'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans2 = PETFiles;
matlabbatch{1}.spm.stats.factorial_design.des.t2.dept = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.variance = 1;
matlabbatch{1}.spm.stats.factorial_design.des.t2.gmsca = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.ancova = 0;
matlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.im = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.em = {'D:\thk\thk_codes\mask_20180209.nii'};
matlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;
matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'P>T';
matlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = [1 -1];
matlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.name = 'P<T';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.weights = [-1 1];
matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 0;
spm_jobman('run',matlabbatch);
clear matlabbatch
% SUVR without PETPVC (SUVwrrns)
fprintf(1,'SUVR without PETPVC\n')
PETFiles = [];
for isub = 1:size(data,2)-1
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwrrns',data(isub).id,'.+60.nii')))
PETFiles = [PETFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwrrns',data(isub).id,'.+60.nii')))];
end
end
matlabbatch{1}.spm.stats.factorial_design.dir = {'d:\thk\RES_SUVR_woPVC'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans1 = {'d:\thk\COF999\PET\sSUVRwrrnsCOF999_b47_2d88_de10_01010001_40-60.nii,1'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans2 = PETFiles;
matlabbatch{1}.spm.stats.factorial_design.des.t2.dept = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.variance = 1;
matlabbatch{1}.spm.stats.factorial_design.des.t2.gmsca = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.ancova = 0;
matlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.im = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.em = {'D:\thk\thk_codes\mask_20180209.nii'};
matlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;
matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'P>T';
matlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = [1 -1];
matlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.name = 'P<T';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.weights = [-1 1];
matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 0;
spm_jobman('run',matlabbatch);
clear matlabbatch
% SUVR with PETPVC
fprintf(1,'SUVR with PETPVC\n')
PETFiles = [];
for isub = 1:size(data,2)
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwPrrns',data(isub).id,'.+\.nii')))
PETFiles = [PETFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwPrrns',data(isub).id,'.+\.nii')))];
end
end
matlabbatch{1}.spm.stats.factorial_design.dir = {'d:\thk\RES_SUVR_wPVC'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans1 = {'d:\thk\COF999\PET\sSUVRwPrrnsCOF999_b47_2d88_de10_01010001_40-60.nii,1'};
matlabbatch{1}.spm.stats.factorial_design.des.t2.scans2 = PETFiles;
matlabbatch{1}.spm.stats.factorial_design.des.t2.dept = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.variance = 1;
matlabbatch{1}.spm.stats.factorial_design.des.t2.gmsca = 0;
matlabbatch{1}.spm.stats.factorial_design.des.t2.ancova = 0;
matlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
matlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.im = 1;
matlabbatch{1}.spm.stats.factorial_design.masking.em = {'D:\thk\thk_codes\mask_20180209.nii'};
matlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;
matlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;
matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;
matlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;
matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));
matlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'P>T';
matlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = [1 -1];
matlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.name = 'P<T';
matlabbatch{3}.spm.stats.con.consess{2}.tcon.weights = [-1 1];
matlabbatch{3}.spm.stats.con.consess{2}.tcon.sessrep = 'none';
matlabbatch{3}.spm.stats.con.delete = 0;
spm_jobman('run',matlabbatch);
clear matlabbatch
%SnPM with PVC
fprintf(1,'SnPM \n')
PETFiles = [];
for isub = 1:size(data,2)-1
if ~isempty(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwPrrns',data(isub).id,'.+60.nii')))
PETFiles = [PETFiles;...
cellstr(spm_select('FPList',fullfile(data(isub).dir,'PET'),strcat('^sSUVRwPrrns',data(isub).id,'.+60.nii')))];
end
end
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.DesignName = '2 Groups: Two Sample T test; 1 scan per subject';
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.DesignFile = 'snpm_bch_ui_TwoSampT';
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.dir = {'d:\thk\RES_SUVR_wPVC_SnPM'};
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.scans1 = {'D:\thk\COF999\PET\sSUVRwPrrnsCOF999_b47_2d88_de10_01010001_40-60.nii'};
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.scans2 = PETFiles;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.cov = struct('c', {}, 'cname', {});
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.nPerm = 5000;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.vFWHM = [0 0 0];
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.bVolm = 1;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.ST.ST_none = 0;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.masking.tm.tm_none = 1;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.masking.im = 1;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.masking.em = {'D:\thk\thk_codes\mask_20180209.nii,1'};
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.globalc.g_omit = 1;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.globalm.gmsca.gmsca_no = 1;
matlabbatch{1}.spm.tools.snpm.des.TwoSampT.globalm.glonorm = 1;
matlabbatch{2}.spm.tools.snpm.cp.snpmcfg(1) = cfg_dep('2 Groups: Two Sample T test; 1 scan per subject: SnPMcfg.mat configuration file', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','SnPMcfg'));
matlabbatch{3}.spm.tools.snpm.inference.SnPMmat(1) = cfg_dep('Compute: SnPM.mat results file', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','SnPM'));
matlabbatch{3}.spm.tools.snpm.inference.Thr.Vox.VoxSig.FWEth = 0.05;
matlabbatch{3}.spm.tools.snpm.inference.Tsign = 1;
matlabbatch{3}.spm.tools.snpm.inference.WriteFiltImg.WF_no = 0;
matlabbatch{3}.spm.tools.snpm.inference.Report = 'MIPtable';
spm_jobman('run',matlabbatch);
clear matlabbatch