spmpath=fileparts(which('spm.m'))
addpath([spmpath filesep 'toolbox']);
addpath([spmpath filesep 'toolbox' filesep 'PPPI']);
addpath('/home/konstantinos/Desktop/task_fMRI_data/');
spm('defaults','fmri')

%Contrast Names
ContrastName1 = 'HCvsLC'
left1 = {'High Context'};
right1 = {'Low Context'};
ContrastName2 = 'HC'
left2 = {'High Context'};
right2 = {'none'};
ContrastName3 = 'LC'
left3 = {'Low Context'};
right3 = {'none'};
ContrastName4 = 'LCvsHC'
left4 = {'Low Context'};
right4 = {'High Context'};

%VOI
VOI= 'VOI_hippo_21_-38_3_r6_mask.nii';
VOI2 = 'VOI_PCC.nii';
VOI3 = 'RightHippo_mask.nii.gz';
VOIName='VOI_hippo_21_-38_3_r6';
Coord=[21 -38 3];
SphereRadious = 6;
mask = 'mask.nii';

% directories
directories.main = ['/home/konstantinos/Desktop/task_fMRI_data/'];
directories.rdir = ['/home/konstantinos/Desktop/task_fMRI_data/S21'];
directories.sdir = ['stats'];
 
% Create VOI

%cd(fullfile(directories.rdir,directories.sdir));
%create_sphere_image(fullfile(directories.rdir,directories.sdir,mask),Coord,{VOIName},SphereRadious)

% Set up the control param structure P which determines the run
%P = struct();
P.subject=directories.sdir;
P.directory=fullfile(directories.rdir,directories.sdir);
P.VOI= fullfile(directories.main,VOI3);
P.Region='right_hippocampus';
P.analysis='psy';
P.method='cond';
P.Estimate=1;
P.contrast=1;
P.extract='eig';
P.Tasks={'1','Rotated Speech','Normal Speech','Low Context','High Context','QuestionDuration'};
P.Weights=0;
P.equalroi=0;
P.FLmask=1;
P.CompContrasts=1;
P.outdir = fullfile(directories.rdir, directories.sdir,'PPI') 
P.ConcatR=1;
SPM = spm_estimate_PPI(P.subject,fullfile(directories.rdir,directories.sdir,'SPM.mat'),P.Region,P.method,P.analysis,P.CompContrasts,0,[],0,0)

% PPI Contrasts
P.Contrasts(1).name= 'HCvsLC'
P.Contrasts(1).left= {'High Context'};
P.Contrasts(1).right= {'Low Context'};
P.Contrasts(1).MinEvents=4;
P.Contrasts(1).STAT='T';

P.Contrasts(2).name = ContrastName2
P.Contrasts(2).left = left2
P.Contrasts(2).right = right2
P.Contrasts(2).MinEvents=4;
P.Contrasts(2).STAT='T';

P.Contrasts(3).name = ContrastName3
P.Contrasts(3).left = left3
P.Contrasts(3).right = right3
P.Contrasts(3).MinEvents=4;
P.Contrasts(3).STAT='T';

P.Contrasts(4).name = ContrastName4
P.Contrasts(4).left = left4
P.Contrasts(4).right = right4
P.Contrasts(4).MinEvents=4;
P.Contrasts(4).STAT='T';


PPPI(P)