input_files=[
'C:/keith/fMRI/manou/cbf_non_kin/subj01_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj01_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj01_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj01_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj01_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj02_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj02_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj02_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj02_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj02_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj03_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj03_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj03_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj03_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj03_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj04_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj04_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj04_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj04_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj04_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj05_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj05_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj05_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj05_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj05_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj06_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj06_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj06_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj06_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj06_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj07_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj07_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj07_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj07_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj07_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj08_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj08_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj08_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj08_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj08_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj09_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj09_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj09_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj09_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj09_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj10_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj10_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj10_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj10_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj10_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj11_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj11_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj11_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj11_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj11_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj12_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj12_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj12_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj12_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj12_-hb_tal_200008160942.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj13_-h1_tal_200008161003.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj13_-h2_tal_200008161025.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj13_-h3_tal_200008161043.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj13_-h4_tal_200008161101.mnc';
'C:/keith/fMRI/manou/cbf_non_kin/subj13_-hb_tal_200008160942.mnc'];
n=65;
layout=reshape(1:n,5,13)
clf;
view_slices(input_files,[],[],21,1:n,[0 40000],layout)
saveas(gcf,'c:/keith/fmristat/figs_pet/fignonnorm.jpg')

input_files_norm=[input_files(:,1:32) repmat('normalized/',n,1) input_files(:,33:size(input_files,2))]
for i=1:n 
   normalize(input_files(i,:),input_files_norm(i,:));
end
clf;
view_slices(input_files_norm,[],[],21,1:n,[0 1.5],layout)
saveas(gcf,'c:/keith/fmristat/figs_pet/fignorm.jpg')

X=[kron(eye(13),ones(5,1)) kron(ones(13,1),eye(5))];
X=X(:,1:17);
num2str(X)

contrast=[mean(X,1); zeros(4,13) eye(4)]
output=[repmat('c:/keith/fMRI/manou/cbf_non_kin_smoother_',5,1) num2str((0:4)')]
which_stats='_t _ef _sd _fwhm'
multistat(input_files_norm,[],[],[],X,contrast,output,which_stats);

mask='c:/keith/fMRI/manou/cbf_non_kin_smoother_0_ef.mnc'
clf;
view_slices('c:/keith/fMRI/manou/cbf_non_kin_smoother_3_ef.mnc',mask,0.65,[0:5:79]) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormef.jpg')
clf;
view_slices('c:/keith/fMRI/manou/cbf_non_kin_smoother_3_sd.mnc',mask,0.65,[0:5:79]) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormsd.jpg')
clf;
view_slices('c:/keith/fMRI/manou/cbf_non_kin_smoother_3_t.mnc',mask,0.65,[0:5:79]) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormt.jpg')
clf;
view_slices('c:/keith/fMRI/manou/cbf_non_kin_smoother_0_fwhm.mnc',mask,0.65,[0:5:79],1,[5 15]) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormfwhm.jpg')

m=['c:/keith/fMRI/manou/cbf_non_kin_smoother_1_t.mnc';
   'c:/keith/fMRI/manou/cbf_non_kin_smoother_2_t.mnc';
   'c:/keith/fMRI/manou/cbf_non_kin_smoother_3_t.mnc';
   'c:/keith/fMRI/manou/cbf_non_kin_smoother_4_t.mnc']
clf;
view_slices(m,mask,0.65,64:66,1:4) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormt1234.jpg')

stat_summary('c:/keith/fMRI/manou/cbf_non_kin_smoother_3_t.mnc', ...
   'c:/keith/fMRI/manou/cbf_non_kin_smoother_0_fwhm.mnc',[],mask,0.65);
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormp.jpg')

keep=[3 5 8 10 13 15 18 20 23 25 28 30 33 35 38 40 43 45 48 50 53 55 58 60 63 65]
input_files_norm3b=input_files_norm(keep,:)
X1=[kron(eye(13),ones(2,1)) kron(ones(13,1),eye(2))];
X1=X1(:,1:14);
num2str(X1)

contrast1=[zeros(1,13) 1]
output3b='c:/keith/fMRI/manou/cbf_non_kin_smooth_3b'
multistat(input_files_norm3b,[],[],[],X1,contrast1,output3b,which_stats);

m=['c:/keith/fMRI/manou/cbf_non_kin_smoother_3_t.mnc';
   'c:/keith/fMRI/manou/cbf_non_kin_smooth_3b_t.mnc ']
clf;
view_slices(m,mask,0.65,64:66,1:2,[-3 6],[1 2 3; 4 5 6]) 
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormt3b.jpg')

stat_summary('c:/keith/fMRI/manou/cbf_non_kin_smooth_3b_t.mnc', ...
   'c:/keith/fMRI/manou/cbf_non_kin_smooth_3b_fwhm.mnc',[],mask,0.65);
saveas(gcf,'c:/keith/fmristat/figs_pet/fignormp3b.jpg')