<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>SPM8RFXscript</title><revhistory><revision><revnumber>2</revnumber><date>2013-03-08 10:02:52</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>1</revnumber><date>2011-02-18 12:43:35</date><authorinitials>YaaraErez</authorinitials></revision></revhistory></articleinfo><section><title>Group Statistics for Source Space Data in SPM8</title><para>This is a basic script for group statistical analysis of source estimation results in SPM8. It uses previously computed <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/SPM8SourceEstimation">source estimation results</ulink> as input to the SPM8 function batch_spm_anova. You can visualise the results as &quot;glass brains&quot; using the Results function in the SPM8 GUI, or display them on a standard cortical surface using the Render-&gt;Display utility. </para><screen><![CDATA[% 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
]]><![CDATA[
addpath /imaging/local/meg_misc;    % for meg_batch_anova
]]><![CDATA[
% root directory for previously computed source stimation results
pathstem = '/YourDataPath/';
]]><![CDATA[
% output root directory for results
out_dir_stem = '/YourResultDirectory';
]]><![CDATA[
]]><![CDATA[
%% Specify data information for each subject
]]><![CDATA[
subjects{1} = {'meg10_0007', '101206'};
subjects{2} = {'meg10_0008', '101224'};
subjects{3} = {'meg10_0009', '101231'};
]]><![CDATA[
nr_ss = length(subjects);
]]><![CDATA[
%% 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
]]><![CDATA[
nr_contrasts = length( contrasts );
]]><![CDATA[
%% Compute Contrasts
]]><![CDATA[
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
        end;
    end;
]]><![CDATA[
    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
]]><![CDATA[
    fprintf(1, '%s\n', S.outdir);
    batch_spm_anova( S );   % run SPM random effects analysis
    
end;]]></screen></section></article>