function conn_batchexample_Setup;
% example batch process for experiment SETUP. Edit the fields below
% This example defines the information for the attention dataset 
(http://www.fil.ion.ucl.ac.uk/spm/data/attention/)
% Information defined here includes: acquisition TR, number of subjects,
% number of sessions per subject, location of functional and anatomical
% volumes, location of ROI files, location of realignment parameters, and
% definition of a single condition encompassing the entire session

%% BATCH INFORMATION (edit this section)
rootfolder=pwd;
batch.filename=...                   % conn_* project file to be 
created/modified
     fullfile(rootfolder,'conn_attention.mat');

%% EXPERIMENT INFORMATION (edit this section)
batch.Setup.isnew=1;                 % 0: modifies existing project; 
1: creates new proejct
batch.Setup.RT=3.22;                 % TR (in seconds)
batch.Setup.nsubjects=1;             % number of subjects

% functional data files (cell array per subject and sessions): 
batch.Setup.functionals{nsub}{nses} is an array listing the 
(smoothed/normalized/realigned) functional file(s) for subject "nsub" 
and session "nses"
files=dir(fullfile(rootfolder,'functional','wsnffM00587_*.img'));
batch.Setup.functionals{1}{1}=[repmat([fullfile(rootfolder,'functional'),filesep],[length(files),1]),strvcat(files(:).name)];

% anatomical volumes (cell array per subject): 
batch.Setup.structurals{nsub} is an array pointing to the 
(normalized) anatomical volume for subject "nsub"
batch.Setup.structurals{1}=fullfile(rootfolder,'structural','wnsM00587_0002.img');

% roi files (cell array per roi): batch.Setup.rois{nroi} is a string 
pointing to a (normalized) ROI file (if not specified all .nii & .img 
& .tal files in the conn/roi folder will be interpreted as ROI files)
batch.Setup.rois={fullfile(fileparts(which('conn')),'rois','BA.img'), ...
     fullfile(fileparts(which('conn')),'utils','otherrois','V1.img'),...
     fullfile(fileparts(which('conn')),'utils','otherrois','V2.img'),...
     fullfile(fileparts(which('conn')),'utils','otherrois','V5.img'),...
     fullfile(fileparts(which('conn')),'utils','otherrois','PFC.img'),...
     fullfile(fileparts(which('conn')),'utils','otherrois','PPC.img') };

% condition names: cell array of strings (one per condition)
batch.Setup.conditions.names={'Fix','Stat','Natt','Att'};
% batch.Setup.conditions.onsets{ncondition}{nsub}{nses} is an array 
of onset value(s) (in seconds) for condition "ncondition" subject 
"nsub" and sessions "nses"
x=load(fullfile(rootfolder,'conditions.mat'));
batch.Setup.conditions.onsets{1}{1}{1}=3.22*max(0,find(x.fix>[0;x.fix(1:end-1)])-2);
batch.Setup.conditions.onsets{2}{1}{1}=3.22*max(0,find(x.stat>[0;x.stat(1:end-1)])-2);
batch.Setup.conditions.onsets{3}{1}{1}=3.22*max(0,find(x.natt>[0;x.natt(1:end-1)])-2);
batch.Setup.conditions.onsets{4}{1}{1}=3.22*max(0,find(x.att>[0;x.att(1:end-1)])-2);
% batch.Setup.conditions.durations{ncondition}{nsub}{nses} is a value 
defining the duration of each block for condition "ncondition" 
subject "nsub" and sessions "nses" %(note: setting to "inf" is 
equivalent to setting this value to the total session time) "
batch.Setup.conditions.durations{1}{1}{1}=32.2;
batch.Setup.conditions.durations{2}{1}{1}=32.2;
batch.Setup.conditions.durations{3}{1}{1}=32.2;
batch.Setup.conditions.durations{4}{1}{1}=32.2;

% names of temporal (first-level) covariates
batch.Setup.covariates.names={'sessions'};
% cell array of strings (one per covariate and subject and 
condition): batch.Setup.covariates.files{ncovariate}{nsub}{nses} is 
an array pointing the a file defining the covariate "ncoviarate" for 
subject "nsub" and sessions "nses" (note: valid files are .txt or 
.mat files and should contain as many rows as scans for each given 
subject/session)
X=kron(eye(4),ones(90,1));save(fullfile(rootfolder,'sessions.mat'),'X');
batch.Setup.covariates.files{1}{1}{1}=fullfile(rootfolder,'sessions.mat');

batch.Setup.done=1;                 % 0: only edits project fields 
(do not run Setup->'Done'); 1: run Setup->'Done'
                                     % 1: Performs initial steps 
(segmentation, data extraction, etc.) on the defined experiment 
(equivalent to pressing "Done" in the gui "Setup" window)
                                     % set to 0 if you prefer to 
further inspect/edit the experiment information in the gui before 
performing this step
batch.Setup.overwrite='Yes';        % overwrite existing results if 
they exist (set to 'No' if you want to skip preprocessing steps for 
subjects/ROIs already analyzed; if in doubt set to 'Yes')
                                     % For example you would set this 
field to 'No' if you have already run this script and later you add a 
few more subjets and/or ROIs and want to run this modified script 
again without having the existing subjects unnecessarily reanalyzed.
                                     % note: removing some subjects 
needs to be done through the gui, if done through the batch you need 
to set overwrite to 'Yes'
conn_batch(batch);