SPM8RFXscript - Meg Wiki
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Group Statistics for Source Space Data in SPM8

This is a basic script for group statistical analysis of source estimation results in SPM8. It uses previously computed source estimation results as input to the SPM8 function batch_spm_anova. You can visualise the results as "glass brains" using the Results function in the SPM8 GUI, or display them on a standard cortical surface using the Render->Display utility.

% to be run in SPM 8 EEG
% runs group statistics on files in "imgfiles", using batch_spm_anova.m
% output written into directory "outdir" (RFX)
% OH, Feb 2010

addpath /imaging/local/meg_misc;    % for meg_batch_anova

% root directory for previously computed source stimation results
pathstem = '/YourDataPath/';

% output root directory for results
out_dir_stem = '/YourResultDirectory';

%% Specify data information for each subject

subjects{1} = {'meg10_0007', '101206'};
subjects{2} = {'meg10_0008', '101224'};
subjects{3} = {'meg10_0009', '101231'};

nr_ss = length(subjects);

%% Define contrasts (depends on how you named output of source estimation)
clear contrasts;
contrasts{1} = {'Mmacespm8_block1_raw_ssstf_raw_1_t100_200_f_7.nii', 'Mmacespm8_block1_raw_ssstf_raw_1_t100_200_f_8.nii', 'CON7vsCON8'};  % Condition 7 vs Condition 8
contrasts{2} = {'Mmacespm8_block1_raw_ssstf_raw_1_t100_200_f_1.nii', 'Mmacespm8_block1_raw_ssstf_raw_1_t100_200_f_2.nii', 'CON1vsCON2'};  % Condition 1 vs Condition 2

nr_contrasts = length( contrasts );

%% Compute Contrasts

for cc = 1:nr_contrasts,        % contrast by contrast
    clear imgfiles;
    for ss = 1:nr_ss,           % subject by subject
        nr_conds = length( contrasts{cc} );
        for con = 1:nr_conds-1, % condition by condition 
            imgfiles{1}{ss}(con,:) = fullfile( pathstem, subjects{ss}{1}, subjects{ss}{2}, contrasts{cc}{con} );    % define full filename

    S = spm_get_defaults;   % get SPM default analysis parameters
    S.imgfiles = imgfiles;  % files for this contrast
    S.outdir = fullfile( out_dir_stem, contrasts{cc}{nr_conds} );   % output directory for this contrast

    fprintf(1, '%s\n', S.outdir);
    batch_spm_anova( S );   % run SPM random effects analysis

CbuMeg: SPM8RFXscript (last edited 2013-03-08 10:02:52 by localhost)