addpath('/gpfs/apps/x86_64-rhel6/freesurfer/5.3.0/freesurfer/matlab')
addpath('/gpfs/home/jtl190/matlab/lme/Qdec')
addpath('/gpfs/home/jtl190/matlab/lme/univariate')
addpath('/gpfs/home/jtl190/matlab/lme/mass_univariate')
addpath('/gpfs/home/jtl190/matlab/lme')
addpath('/gpfs/home/jtl190/matlab/lme/LME_data/Qdec_analysis_files')
cd('/gpfs/home/jtl190/matlab/lme/LME_data')
[Y,mri] = fs_read_Y('rh.volume.mgh');
Qdec = fReadQdec_sf('qdec_multivariate_nocov.csv');
sID_Cov = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
sID = Qdec(2:end,1);
Qdec = rmQdecCol(Qdec,1);
M = Qdec2num(Qdec);
[M,Y,ni] = sortData(M,1,Y,sID);
rhsphere = fs_read_surf('rh.sphere');
rhcortex = fs_read_label('rh.cortex.label');
X = [ones(length(M),1) M(:,1:3) M(:,1).*M(:,2)];
[rhTh0,rhRe] = lme_mass_fit_EMinit(X,[1],Y,ni,rhcortex,3);
[rhRgs,rhRgMeans] = lme_mass_RgGrow(rhsphere,rhRe,rhTh0,rhcortex,2,95)
rhstats = lme_mass_fit_Rgw(X,[1],Y,ni,rhTh0,rhRgs,rhsphere);
CM.C = [0 1 0 0 0]
F_rhstats = lme_mass_F(rhstats,CM);
save('F_rhstats_data_time.mat', 'F_rhstats');
fs_write_fstats(F_rhstats,mri,'rh_time_sig.mgh','sig');
dvtx = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);
[detvtx,sided_pval,pth] = lme_mass_FDR2(F_rhstats.pval,F_rhstats.sgn,rhcortex,0.05,0);
mri1 = mri;
mri1.volsz(4) = 1;
fs_write_Y(sided_pval,mri1,'rh_time_spval.mgh');
quit