function restingstate_conn
% This example prompts the user to select one subject functional series
% (one resting state session) and one anatomical volume, and performs all 
% standard SPM spatial preprocessing steps (realignment,coregistration,
% normalization,smoothing) and connectivity analyses using all the BA areas
% as sources
%

%% batch preprocessing for single-subject single-session data 

addpath(genpath('/opt/spm8'));
addpath(genpath('/opt/conn/conn'));

cwd=pwd;
rootfolder=pwd;

% Selects functional / anatomical volumes
%FUNCTIONAL_FILE=cellstr(conn_dir('../data/rest/*.nii'));
%if isempty(FUNCTIONAL_FILE),return;end
%STRUCTURAL_FILE=cellstr(conn_dir('../data/structural/*.nii'));
%if isempty(STRUCTURAL_FILE),return;end


%% CONN New experiment
batch.filename=fullfile(pwd,'TMSGamblingANOVA.mat');
if ~isempty(dir(batch.filename)), 
    Ransw=questdlg('TMSGamblingANOVA project already exists, Overwrite?','warning','Yes','No','No');
    if ~strcmp(Ransw,'Yes'), return; end; 
end
% FUNCTIONALS START
%batch.New.functionals{1}{1}=FUNCTIONAL_FILE;
batch.New.functionals{1}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S0948CNP1/data/gamble/*.nii'));
batch.New.functionals{2}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S1449HWH1/data/gamble/*.nii'));
batch.New.functionals{3}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S1941NEN1/data/gamble/*.nii'));
batch.New.functionals{4}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S2698OZH1/data/gamble/*.nii'));
batch.New.functionals{5}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S4068HQW1/data/gamble/*.nii'));
batch.New.functionals{6}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S5455JXZ1/data/gamble/*.nii'));
batch.New.functionals{7}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S6741ZNQ1/data/gamble/*.nii'));
batch.New.functionals{8}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S7618NVM1/data/gamble/*.nii'));
batch.New.functionals{9}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S8566SWD1/data/gamble/*.nii'));
batch.New.functionals{10}{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S9189WZM1/data/gamble/*.nii'));
batch.New.functionals{1}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S0948CNP2/data/gamble/*.nii'));
batch.New.functionals{2}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S1449HWH2/data/gamble/*.nii'));
batch.New.functionals{3}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S1941NEN2/data/gamble/*.nii'));
batch.New.functionals{4}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S2698OZH2/data/gamble/*.nii'));
batch.New.functionals{5}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S4068HQW2/data/gamble/*.nii'));
batch.New.functionals{6}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S5455JXZ2/data/gamble/*.nii'));
batch.New.functionals{7}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S6741ZNQ3/data/gamble/*.nii'));
batch.New.functionals{8}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S7618NVM2/data/gamble/*.nii'));
batch.New.functionals{9}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S8566SWD2/data/gamble/*.nii'));
batch.New.functionals{10}{2}=cellstr(conn_dir('../TMSGamblingPatientTxPost/TMSGamblingPrePostTx/S9189WZM2/data/gamble/*.nii'));
batch.New.functionals{11}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S0284TFO1/data/gamble/*.nii'));
batch.New.functionals{12}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1047ULP1/data/gamble/*.nii'));
batch.New.functionals{13}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1677SEO1/data/gamble/*.nii'));
batch.New.functionals{14}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1880LHD1/data/gamble/*.nii'));
batch.New.functionals{15}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S2177FFZ1/data/gamble/*.nii'));
batch.New.functionals{16}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S9446RIF1/data/gamble/*.nii'));
batch.New.functionals{17}{1}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S9510RBR1/data/gamble/*.nii'));
batch.New.functionals{11}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S0284TFO2/data/gamble/*.nii'));
batch.New.functionals{12}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S1047ULP2/data/gamble/*.nii'));
batch.New.functionals{13}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S1677SEO2/data/gamble/*.nii'));
batch.New.functionals{14}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S1880LHD2/data/gamble/*.nii'));
batch.New.functionals{15}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S2177FFZ2/data/gamble/*.nii'));
batch.New.functionals{16}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S9446RIF2/data/gamble/*.nii'));
batch.New.functionals{17}{2}=cellstr(conn_dir('../TMSGamblingPatientShamPost/TMSGamblingAllSham/S9510RBR2/data/gamble/*.nii'));
% FUNCTIONALS END
% STRUCTURALS START
%batch.New.structurals{1}=STRUCTURAL_FILE;
batch.New.structurals{1}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S0948CNP1/data/structural/*.nii'));
batch.New.structurals{2}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S1449HWH1/data/structural/*.nii'));
batch.New.structurals{3}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S1941NEN1/data/structural/*.nii'));
batch.New.structurals{4}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S2698OZH1/data/structural/*.nii'));
batch.New.structurals{5}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S4068HQW1/data/structural/*.nii'));
batch.New.structurals{6}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S5455JXZ1/data/structural/*.nii'));
batch.New.structurals{7}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S6741ZNQ1/data/structural/*.nii'));
batch.New.structurals{8}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S7618NVM1/data/structural/*.nii'));
batch.New.structurals{9}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S8566SWD1/data/structural/*.nii'));
batch.New.structurals{10}=cellstr(conn_dir('../TMSGamblingPatientTxPre/TMSGamblingPrePostTx/S9189WZM1/data/structural/*.nii'));
batch.New.structurals{11}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S0284TFO1/data/structural/*.nii'));
batch.New.structurals{12}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1047ULP1/data/structural/*.nii'));
batch.New.structurals{13}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1677SEO1/data/structural/*.nii'));
batch.New.structurals{14}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S1880LHD1/data/structural/*.nii'));
batch.New.structurals{15}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S2177FFZ1/data/structural/*.nii'));
batch.New.structurals{16}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S9446RIF1/data/structural/*.nii'));
batch.New.structurals{17}=cellstr(conn_dir('../TMSGamblingPatientShamPre/TMSGamblingAllSham/S9510RBR1/data/structural/*.nii'));
% STRUCTURALS END

batch.New.steps={'Segmentation','Realignment','Coregistration','Normalization','Smoothing','Initialization'};
batch.New.FWHM=8;
batch.New.VOX=2;
%% CONN Setup
batch.Setup.nsubjects=17;
batch.Setup.RT=1.86;
batch.Setup.rois.names={'BA','rDLPFC','rAmygdala','Hammers'};
batch.Setup.rois.files{1}='/opt/conn/conn13p/BA.img';
batch.Setup.rois.files{2}='/opt/conn/conn13p/rDLPFC.nii';
batch.Setup.rois.files{3}='/opt/conn/conn13p/rightAmygdala.nii';
batch.Setup.rois.files{4}='/opt/conn/conn13p/HammersAtlas.img';
batch.Setup.subjects.names={'Treatment','Sham'};
batch.Setup.subjects.effects{1}=[1;1;1;1;1;1;1;1;1;1;0;0;0;0;0;0;0];
batch.Setup.subjects.effects{2}=[0;0;0;0;0;0;0;0;0;0;1;1;1;1;1;1;1];
% CONDITIONS START
batch.Setup.conditions.names={'rest_pre','even_pre','lose_pre','rest_post','even_post','lose_post'};
%batch.Setup.conditions.onsets{1}{1}{1}=0;
%batch.Setup.conditions.durations{1}{1}{1}=inf;
% subject 1, session 1
batch.Setup.conditions.onsets{1}{1}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{1}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{1}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{1}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{1}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{1}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{1}{1} = 0;
batch.Setup.conditions.onsets{5}{1}{1} = 0;
batch.Setup.conditions.onsets{6}{1}{1} = 0;
batch.Setup.conditions.durations{4}{1}{1} = inf;
batch.Setup.conditions.durations{5}{1}{1} = inf;
batch.Setup.conditions.durations{6}{1}{1} = inf;
% subject 2, session 1
batch.Setup.conditions.onsets{1}{2}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{2}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{2}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{2}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{2}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{2}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{2}{1} = 0;
batch.Setup.conditions.onsets{5}{2}{1} = 0;
batch.Setup.conditions.onsets{6}{2}{1} = 0;
batch.Setup.conditions.durations{4}{2}{1} = inf;
batch.Setup.conditions.durations{5}{2}{1} = inf;
batch.Setup.conditions.durations{6}{2}{1} = inf;
% subject 3, session 1
batch.Setup.conditions.onsets{1}{3}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{3}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{3}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{3}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{3}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{3}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{3}{1} = 0;
batch.Setup.conditions.onsets{5}{3}{1} = 0;
batch.Setup.conditions.onsets{6}{3}{1} = 0;
batch.Setup.conditions.durations{4}{3}{1} = inf;
batch.Setup.conditions.durations{5}{3}{1} = inf;
batch.Setup.conditions.durations{6}{3}{1} = inf;
% subject 4, session 1
batch.Setup.conditions.onsets{1}{4}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{4}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{4}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{4}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{4}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{4}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{4}{1} = 0;
batch.Setup.conditions.onsets{5}{4}{1} = 0;
batch.Setup.conditions.onsets{6}{4}{1} = 0;
batch.Setup.conditions.durations{4}{4}{1} = inf;
batch.Setup.conditions.durations{5}{4}{1} = inf;
batch.Setup.conditions.durations{6}{4}{1} = inf;
% subject 5, session 1
batch.Setup.conditions.onsets{1}{5}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{5}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{5}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{5}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{5}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{5}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{5}{1} = 0;
batch.Setup.conditions.onsets{5}{5}{1} = 0;
batch.Setup.conditions.onsets{6}{5}{1} = 0;
batch.Setup.conditions.durations{4}{5}{1} = inf;
batch.Setup.conditions.durations{5}{5}{1} = inf;
batch.Setup.conditions.durations{6}{5}{1} = inf;
% subject 6, session 1
batch.Setup.conditions.onsets{1}{6}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{6}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{6}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{6}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{6}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{6}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{6}{1} = 0;
batch.Setup.conditions.onsets{5}{6}{1} = 0;
batch.Setup.conditions.onsets{6}{6}{1} = 0;
batch.Setup.conditions.durations{4}{6}{1} = inf;
batch.Setup.conditions.durations{5}{6}{1} = inf;
batch.Setup.conditions.durations{6}{6}{1} = inf;
% subject 7, session 1
batch.Setup.conditions.onsets{1}{7}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{7}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{7}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{7}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{7}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{7}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{7}{1} = 0;
batch.Setup.conditions.onsets{5}{7}{1} = 0;
batch.Setup.conditions.onsets{6}{7}{1} = 0;
batch.Setup.conditions.durations{4}{7}{1} = inf;
batch.Setup.conditions.durations{5}{7}{1} = inf;
batch.Setup.conditions.durations{6}{7}{1} = inf;
% subject 8, session 1
batch.Setup.conditions.onsets{1}{8}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{8}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{8}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{8}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{8}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{8}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{8}{1} = 0;
batch.Setup.conditions.onsets{5}{8}{1} = 0;
batch.Setup.conditions.onsets{6}{8}{1} = 0;
batch.Setup.conditions.durations{4}{8}{1} = inf;
batch.Setup.conditions.durations{5}{8}{1} = inf;
batch.Setup.conditions.durations{6}{8}{1} = inf;
% subject 9, session 1
batch.Setup.conditions.onsets{1}{9}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{9}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{9}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{9}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{9}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{9}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{9}{1} = 0;
batch.Setup.conditions.onsets{5}{9}{1} = 0;
batch.Setup.conditions.onsets{6}{9}{1} = 0;
batch.Setup.conditions.durations{4}{9}{1} = inf;
batch.Setup.conditions.durations{5}{9}{1} = inf;
batch.Setup.conditions.durations{6}{9}{1} = inf;
% subject 10, session 1
batch.Setup.conditions.onsets{1}{10}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{10}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{10}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{10}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{10}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{10}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{10}{1} = 0;
batch.Setup.conditions.onsets{5}{10}{1} = 0;
batch.Setup.conditions.onsets{6}{10}{1} = 0;
batch.Setup.conditions.durations{4}{10}{1} = inf;
batch.Setup.conditions.durations{5}{10}{1} = inf;
batch.Setup.conditions.durations{6}{10}{1} = inf;
% subject 11, session 1
batch.Setup.conditions.onsets{1}{11}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{11}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{11}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{11}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{11}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{11}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{11}{1} = 0;
batch.Setup.conditions.onsets{5}{11}{1} = 0;
batch.Setup.conditions.onsets{6}{11}{1} = 0;
batch.Setup.conditions.durations{4}{11}{1} = inf;
batch.Setup.conditions.durations{5}{11}{1} = inf;
batch.Setup.conditions.durations{6}{11}{1} = inf;
% subject 12, session 1
batch.Setup.conditions.onsets{1}{12}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{12}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{12}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{12}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{12}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{12}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{12}{1} = 0;
batch.Setup.conditions.onsets{5}{12}{1} = 0;
batch.Setup.conditions.onsets{6}{12}{1} = 0;
batch.Setup.conditions.durations{4}{12}{1} = inf;
batch.Setup.conditions.durations{5}{12}{1} = inf;
batch.Setup.conditions.durations{6}{12}{1} = inf;
% subject 13, session 1
batch.Setup.conditions.onsets{1}{13}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{13}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{13}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{13}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{13}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{13}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{13}{1} = 0;
batch.Setup.conditions.onsets{5}{13}{1} = 0;
batch.Setup.conditions.onsets{6}{13}{1} = 0;
batch.Setup.conditions.durations{4}{13}{1} = inf;
batch.Setup.conditions.durations{5}{13}{1} = inf;
batch.Setup.conditions.durations{6}{13}{1} = inf;
% subject 14, session 1
batch.Setup.conditions.onsets{1}{14}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{14}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{14}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{14}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{14}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{14}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{14}{1} = 0;
batch.Setup.conditions.onsets{5}{14}{1} = 0;
batch.Setup.conditions.onsets{6}{14}{1} = 0;
batch.Setup.conditions.durations{4}{14}{1} = inf;
batch.Setup.conditions.durations{5}{14}{1} = inf;
batch.Setup.conditions.durations{6}{14}{1} = inf;
% subject 15, session 1
batch.Setup.conditions.onsets{1}{15}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{15}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{15}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{15}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{15}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{15}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{15}{1} = 0;
batch.Setup.conditions.onsets{5}{15}{1} = 0;
batch.Setup.conditions.onsets{6}{15}{1} = 0;
batch.Setup.conditions.durations{4}{15}{1} = inf;
batch.Setup.conditions.durations{5}{15}{1} = inf;
batch.Setup.conditions.durations{6}{15}{1} = inf;
% subject 16, session 1
batch.Setup.conditions.onsets{1}{16}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{16}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{16}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{16}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{16}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{16}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{16}{1} = 0;
batch.Setup.conditions.onsets{5}{16}{1} = 0;
batch.Setup.conditions.onsets{6}{16}{1} = 0;
batch.Setup.conditions.durations{4}{16}{1} = inf;
batch.Setup.conditions.durations{5}{16}{1} = inf;
batch.Setup.conditions.durations{6}{16}{1} = inf;
% subject 17, session 1
batch.Setup.conditions.onsets{1}{17}{1}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{2}{17}{1}=[0,138,230,276];
batch.Setup.conditions.onsets{3}{17}{1}=[46,92,184,322];
batch.Setup.conditions.durations{1}{17}{1}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{2}{17}{1}=[28,28,28,28];
batch.Setup.conditions.durations{3}{17}{1}=[28,28,28,28];
batch.Setup.conditions.onsets{4}{17}{1} = 0;
batch.Setup.conditions.onsets{5}{17}{1} = 0;
batch.Setup.conditions.onsets{6}{17}{1} = 0;
batch.Setup.conditions.durations{4}{17}{1} = inf;
batch.Setup.conditions.durations{5}{17}{1} = inf;
batch.Setup.conditions.durations{6}{17}{1} = inf;
% subject 1, session 2
batch.Setup.conditions.onsets{1}{1}{2} = 0;
batch.Setup.conditions.onsets{2}{1}{2} = 0;
batch.Setup.conditions.onsets{3}{1}{2} = 0;
batch.Setup.conditions.durations{1}{1}{2} = inf;
batch.Setup.conditions.durations{2}{1}{2} = inf;
batch.Setup.conditions.durations{3}{1}{2} = inf;
batch.Setup.conditions.onsets{4}{1}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{1}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{1}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{1}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{1}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{1}{2}=[28,28,28,28];
% subject 2, session 2
batch.Setup.conditions.onsets{1}{2}{2} = 0;
batch.Setup.conditions.onsets{2}{2}{2} = 0;
batch.Setup.conditions.onsets{3}{2}{2} = 0;
batch.Setup.conditions.durations{1}{2}{2} = inf;
batch.Setup.conditions.durations{2}{2}{2} = inf;
batch.Setup.conditions.durations{3}{2}{2} = inf;
batch.Setup.conditions.onsets{4}{2}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{2}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{2}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{2}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{2}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{2}{2}=[28,28,28,28];
% subject 3, session 2
batch.Setup.conditions.onsets{1}{3}{2} = 0;
batch.Setup.conditions.onsets{2}{3}{2} = 0;
batch.Setup.conditions.onsets{3}{3}{2} = 0;
batch.Setup.conditions.durations{1}{3}{2} = inf;
batch.Setup.conditions.durations{2}{3}{2} = inf;
batch.Setup.conditions.durations{3}{3}{2} = inf;
batch.Setup.conditions.onsets{4}{3}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{3}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{3}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{3}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{3}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{3}{2}=[28,28,28,28];
% subject 4, session 2
batch.Setup.conditions.onsets{1}{4}{2} = 0;
batch.Setup.conditions.onsets{2}{4}{2} = 0;
batch.Setup.conditions.onsets{3}{4}{2} = 0;
batch.Setup.conditions.durations{1}{4}{2} = inf;
batch.Setup.conditions.durations{2}{4}{2} = inf;
batch.Setup.conditions.durations{3}{4}{2} = inf;
batch.Setup.conditions.onsets{4}{4}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{4}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{4}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{4}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{4}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{4}{2}=[28,28,28,28];
% subject 5, session 2
batch.Setup.conditions.onsets{1}{5}{2} = 0;
batch.Setup.conditions.onsets{2}{5}{2} = 0;
batch.Setup.conditions.onsets{3}{5}{2} = 0;
batch.Setup.conditions.durations{1}{5}{2} = inf;
batch.Setup.conditions.durations{2}{5}{2} = inf;
batch.Setup.conditions.durations{3}{5}{2} = inf;
batch.Setup.conditions.onsets{4}{5}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{5}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{5}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{5}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{5}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{5}{2}=[28,28,28,28];
% subject 6, session 2
batch.Setup.conditions.onsets{1}{6}{2} = 0;
batch.Setup.conditions.onsets{2}{6}{2} = 0;
batch.Setup.conditions.onsets{3}{6}{2} = 0;
batch.Setup.conditions.durations{1}{6}{2} = inf;
batch.Setup.conditions.durations{2}{6}{2} = inf;
batch.Setup.conditions.durations{3}{6}{2} = inf;
batch.Setup.conditions.onsets{4}{6}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{6}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{6}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{6}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{6}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{6}{2}=[28,28,28,28];
% subject 7, session 2
batch.Setup.conditions.onsets{1}{7}{2} = 0;
batch.Setup.conditions.onsets{2}{7}{2} = 0;
batch.Setup.conditions.onsets{3}{7}{2} = 0;
batch.Setup.conditions.durations{1}{7}{2} = inf;
batch.Setup.conditions.durations{2}{7}{2} = inf;
batch.Setup.conditions.durations{3}{7}{2} = inf;
batch.Setup.conditions.onsets{4}{7}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{7}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{7}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{7}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{7}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{7}{2}=[28,28,28,28];
% subject 8, session 2
batch.Setup.conditions.onsets{1}{8}{2} = 0;
batch.Setup.conditions.onsets{2}{8}{2} = 0;
batch.Setup.conditions.onsets{3}{8}{2} = 0;
batch.Setup.conditions.durations{1}{8}{2} = inf;
batch.Setup.conditions.durations{2}{8}{2} = inf;
batch.Setup.conditions.durations{3}{8}{2} = inf;
batch.Setup.conditions.onsets{4}{8}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{8}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{8}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{8}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{8}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{8}{2}=[28,28,28,28];
% subject 9, session 2
batch.Setup.conditions.onsets{1}{9}{2} = 0;
batch.Setup.conditions.onsets{2}{9}{2} = 0;
batch.Setup.conditions.onsets{3}{9}{2} = 0;
batch.Setup.conditions.durations{1}{9}{2} = inf;
batch.Setup.conditions.durations{2}{9}{2} = inf;
batch.Setup.conditions.durations{3}{9}{2} = inf;
batch.Setup.conditions.onsets{4}{9}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{9}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{9}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{9}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{9}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{9}{2}=[28,28,28,28];
% subject 10, session 2
batch.Setup.conditions.onsets{1}{10}{2} = 0;
batch.Setup.conditions.onsets{2}{10}{2} = 0;
batch.Setup.conditions.onsets{3}{10}{2} = 0;
batch.Setup.conditions.durations{1}{10}{2} = inf;
batch.Setup.conditions.durations{2}{10}{2} = inf;
batch.Setup.conditions.durations{3}{10}{2} = inf;
batch.Setup.conditions.onsets{4}{10}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{10}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{10}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{10}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{10}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{10}{2}=[28,28,28,28];
% subject 11, session 2
batch.Setup.conditions.onsets{1}{11}{2} = 0;
batch.Setup.conditions.onsets{2}{11}{2} = 0;
batch.Setup.conditions.onsets{3}{11}{2} = 0;
batch.Setup.conditions.durations{1}{11}{2} = inf;
batch.Setup.conditions.durations{2}{11}{2} = inf;
batch.Setup.conditions.durations{3}{11}{2} = inf;
batch.Setup.conditions.onsets{4}{11}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{11}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{11}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{11}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{11}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{11}{2}=[28,28,28,28];
% subject 12, session 2
batch.Setup.conditions.onsets{1}{12}{2} = 0;
batch.Setup.conditions.onsets{2}{12}{2} = 0;
batch.Setup.conditions.onsets{3}{12}{2} = 0;
batch.Setup.conditions.durations{1}{12}{2} = inf;
batch.Setup.conditions.durations{2}{12}{2} = inf;
batch.Setup.conditions.durations{3}{12}{2} = inf;
batch.Setup.conditions.onsets{4}{12}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{12}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{12}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{12}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{12}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{12}{2}=[28,28,28,28];
% subject 13, session 2
batch.Setup.conditions.onsets{1}{13}{2} = 0;
batch.Setup.conditions.onsets{2}{13}{2} = 0;
batch.Setup.conditions.onsets{3}{13}{2} = 0;
batch.Setup.conditions.durations{1}{13}{2} = inf;
batch.Setup.conditions.durations{2}{13}{2} = inf;
batch.Setup.conditions.durations{3}{13}{2} = inf;
batch.Setup.conditions.onsets{4}{13}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{13}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{13}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{13}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{13}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{13}{2}=[28,28,28,28];
% subject 14, session 2
batch.Setup.conditions.onsets{1}{14}{2} = 0;
batch.Setup.conditions.onsets{2}{14}{2} = 0;
batch.Setup.conditions.onsets{3}{14}{2} = 0;
batch.Setup.conditions.durations{1}{14}{2} = inf;
batch.Setup.conditions.durations{2}{14}{2} = inf;
batch.Setup.conditions.durations{3}{14}{2} = inf;
batch.Setup.conditions.onsets{4}{14}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{14}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{14}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{14}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{14}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{14}{2}=[28,28,28,28];
% subject 15, session 2
batch.Setup.conditions.onsets{1}{15}{2} = 0;
batch.Setup.conditions.onsets{2}{15}{2} = 0;
batch.Setup.conditions.onsets{3}{15}{2} = 0;
batch.Setup.conditions.durations{1}{15}{2} = inf;
batch.Setup.conditions.durations{2}{15}{2} = inf;
batch.Setup.conditions.durations{3}{15}{2} = inf;
batch.Setup.conditions.onsets{4}{15}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{15}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{15}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{15}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{15}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{15}{2}=[28,28,28,28];
% subject 16, session 2
batch.Setup.conditions.onsets{1}{16}{2} = 0;
batch.Setup.conditions.onsets{2}{16}{2} = 0;
batch.Setup.conditions.onsets{3}{16}{2} = 0;
batch.Setup.conditions.durations{1}{16}{2} = inf;
batch.Setup.conditions.durations{2}{16}{2} = inf;
batch.Setup.conditions.durations{3}{16}{2} = inf;
batch.Setup.conditions.onsets{4}{16}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{16}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{16}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{16}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{16}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{16}{2}=[28,28,28,28];
% subject 17, session 2
batch.Setup.conditions.onsets{1}{17}{2} = 0;
batch.Setup.conditions.onsets{2}{17}{2} = 0;
batch.Setup.conditions.onsets{3}{17}{2} = 0;
batch.Setup.conditions.durations{1}{17}{2} = inf;
batch.Setup.conditions.durations{2}{17}{2} = inf;
batch.Setup.conditions.durations{3}{17}{2} = inf;
batch.Setup.conditions.onsets{4}{17}{2}=[28,74,120,166,212,258,304,350];
batch.Setup.conditions.onsets{5}{17}{2}=[0,138,230,276];
batch.Setup.conditions.onsets{6}{17}{2}=[46,92,184,322];
batch.Setup.conditions.durations{4}{17}{2}=[18,18,18,18,18,18,18,18];
batch.Setup.conditions.durations{5}{17}{2}=[28,28,28,28];
batch.Setup.conditions.durations{6}{17}{2}=[28,28,28,28];
% CONDITIONS END
batch.Setup.done=1;
batch.Setup.overwrite='Yes';
%% CONN Preprocessing
batch.Preprocessing.filter=[0.01, 0.1];          % frequency filter (band-pass values, in Hz)
batch.Preprocessing.done=1;
%% CONN Analysis
batch.Analysis.analysis_number=1;       % Sequential number identifying each set of independent first-level analyses
batch.Analysis.measure=1;               % connectivity measure used {1 = 'correlation (bivariate)', 2 = 'correlation (semipartial)', 3 = 'regression (bivariate)', 4 = 'regression (multivariate)';
batch.Analysis.weight=2;                % within-condition weight used {1 = 'none', 2 = 'hrf', 3 = 'hanning';
batch.Analysis.sources={};              % (defaults to all ROIs)
batch.Analysis.done=1;

conn_batch(batch);

%% CONN Display
% launches conn gui to explore results
%conn
%conn('load',fullfile(pwd,'TMSGamblingANOVA.mat'));
%conn gui_results


end