% Second level (multiple subjects) analysis
% Christian Kaul, July 2007
% presented @ Matlab for Cogntive Neuroscience 12/07/07
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% this script assumes a folder structure like this:
%
% exp_name/
% exp_name/s1
% exp_name/s1/structural           % the structural folder contains
% structural, fieldmaps, segmentation,...
% exp_name/s1/structural/ROI       %the ROI folder contains all the area defs, ergo put your amygdala def here
%
% exp_name/s1/localizer_data
% exp_name/s1/localizer_data/run1  % contains functional files
% exp_name/s1/localizer_data/run2
% exp_name/s1/localizer_stats      % contains the SPM, betas, con-images
%
% exp_name/s1/experiment
% exp_name/s1/experiment/run1      % contains functional files
% exp_name/s1/experiment/run2
% exp_name/s1/experiment_stats     % contains the SPM, betas, con-images


% this batch script with perform the following:
% 1) Second level analysis (here: simple ttest for subjects defined
%
clear all

% SPM results directory for each subject is
statsDirName = 'exp_stats';
% Specify root directory
origDir  = 'D:\V1load_motion2';

dataFolder = 'experiment\run';
structuralFolder = 'structural';

% subjects and the number of volumes collected for each run and the name of
% the structural file
subjects = { ...
    '1',  ones(1,48)*48-3, 'ED-MA04903.img'; ...
    '2',  ones(1,48)*48-3, 'GV-MA04904.img'; ...
    '3',  ones(1,48)*48-3, 'HR-sMA04830.img'; ...
    '4',  ones(1,48)*48-3, 'DB-meansMA04771.img'; ...
    '5',  ones(1,48)*48-3, 'AD.img'; ...
    };
% =========================================================================
% =========================================================================
% =========================================================================
% =========================== Second level analysis =======================
% =========================================================================
cd(origDir);
spm fmri
resultsFolder = 'univariate_2nd_level';

% if the intended resultsFolder directory does not exits, make it and go into it
if exist(resultsFolder) ~= 7
    mkdir(resultsFolder);
    cd(resultsFolder);
else
    % if it does exist, go into it and delete its contents.
    % change this for more than one 2nd level test
    cd(resultsFolder);
    delete('*.*');
end
% setup job structure for 2nd level test
% ---------------------------------------------------------------------
for s0 = 1 : size(subjects,1)  % select con image from every subject
    spmDir = [origDir '\s' subjects{s0,1} '\' statsDirName];
    jobs{1}.stats{1}.factorial_design.des.t1.scans    = {[spmDir '\con_0001.img,1']} ;
end

jobs{1}.stats{1}.factorial_design.cov = struct('c',{},'cname',{},'iCFI',{},'iCC',{});
jobs{1}.stats{1}.factorial_design.masking.tm.tm_none = [];
jobs{1}.stats{1}.factorial_design.masking.im = 1;
jobs{1}.stats{1}.factorial_design.masking.em = {};
jobs{1}.stats{1}.factorial_design.globalc.g_omit = [];
jobs{1}.stats{1}.factorial_design.globalm.gmsca.gmsca_no = [];
jobs{1}.stats{1}.factorial_design.globalm.glonorm = 1;
jobs{1}.stats{1}.factorial_design.dir = {[]}
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% run 2nd level test
% ---------------------------------------------------------------------
% save and run job
save second_level.mat jobs
disp(['RUNNING second level test']);
spm_jobman('run','second_level.mat');
clear jobs
cd(origDir);

Published with MATLAB® 7.1