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Script7_Z_Score_features_by_controls.m
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Script7_Z_Score_features_by_controls.m
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%% Script 7. Intersubject normalisation of features - Z-score by controls
clear all
%% Z score patient measures by controls
% Directory of patients
subjects_dir = '~/Desktop/Sophie_study/FCD_study/'
cd(subjects_dir)
setenv SUBJECTS_DIR .
addpath /Applications/freesurfer/matlab/
%change to appropriate prefix
Subs=dir('FCD_*');
subs=cell(length(Subs),1);
for s = 1:length(Subs);
subs{s}=Subs(s).name;
end
% Optional list of patients to be excluded
Remove={'FCD_05'; 'FCD_14';};
ind=find(ismember(subs,Remove));
subs(ind)=[];
% Load cortex label. +1 for freesurfer matlab indexing
Cortex=read_label(['fsaverage_sym'],['lh.cortex']);
Cortex=Cortex(:,1)+1;
Measures={'.thickness_z_on_lh.sm10.mgh'; '.lh-rh.thickness_z.sm10.mgh';...
'.w-g.pct_z_on_lh.sm10.mgh';'.lh-rh.w-g.pct_z.sm10.mgh';...
'.CurvatureDisc_z_on_lh.mgh';'.lh-rh.CurvatureDisc_z.mgh';...
'.curv_on_lh.mgh';'.sulc_on_lh.mgh';...
'.gm_FLAIR_0.75_z_on_lh.sm10.mgh';'.gm_FLAIR_0.5_z_on_lh.sm10.mgh';...
'.gm_FLAIR_0.25_z_on_lh.sm10.mgh';'.gm_FLAIR_0_z_on_lh.sm10.mgh';...
'.wm_FLAIR_0.5_z_on_lh.sm10.mgh';'.wm_FLAIR_1_z_on_lh.sm10.mgh';...
'.lh-rh.gm_FLAIR_0.75_z.sm10.mgh';'.lh-rh.gm_FLAIR_0.5_z.sm10.mgh';...
'.lh-rh.gm_FLAIR_0.25_z.sm10.mgh';'.lh-rh.gm_FLAIR_0_z.sm10.mgh';...
'.lh-rh.wm_FLAIR_0.5_z.sm10.mgh';'.lh-rh.wm_FLAIR_1_z.sm10.mgh'};
% Directory of controls
%change to appropriate control directory and prefix
Control_dir= '/Users/sophie/Desktop/Sophie_study/FCD_study_with_FLAIR/Controls'
cd(Control_dir)
Cons=dir('C_*');
cons=cell(length(Cons),1);
% For each measure normalise by controls
for L = 1:length(Measures);
Normal_C_L=zeros(length(cons),length(Cortex));
Normal_C_R=zeros(length(cons),length(Cortex));
cd(Control_dir)
setenv SUBJECTS_DIR .
for c = 1:length(Cons);
con=Cons(c).name;
% Load measure in controls and extract cortical values
ML_C=MRIread(['',con,'/xhemi/surf/lh',Measures{L},'']);
Normal_C_L(c,:)=ML_C.vol(Cortex);
MR_C=MRIread(['',con,'/xhemi/surf/rh',Measures{L},'']);
Normal_C_R(c,:)=MR_C.vol(Cortex);
end
% Change to patient directory
cd(subjects_dir)
setenv SUBJECTS_DIR .
Measure_L=zeros(length(subs),length(Cortex));
Measure_R=zeros(length(subs),length(Cortex));
for s = 1:length(subs)
sub=subs(s);
sub=cell2mat(sub);
%Load patient data measure for each hemisphere
ML=MRIread(['',sub,'/xhemi/surf/lh',Measures{L},'']);
Measure_L(s,:)=ML.vol(Cortex);
MR=MRIread(['',sub,'/xhemi/surf/rh',Measures{L},'']);
Measure_R(s,:)=MR.vol(Cortex);
end
% Normalise left hemi by controls by mean and std
zMeasure_L = zeros(size(Measure_L));
meanY=nanmean(Normal_C_L,1);
stdY=nanstd(Normal_C_L, 0, 1);
for i = 1 : size(Measure_L,1)
zMeasure_L(i, :) = (Measure_L(i,:) - meanY)./stdY;
end
% Normalise right hemi by controls
zMeasure_R = zeros(size(Measure_R));
meanY=nanmean(Normal_C_R,1);
stdY=nanstd(Normal_C_R, 0, 1);
for i = 1 : size(Measure_R,1)
zMeasure_R(i, :) = (Measure_R(i,:) - meanY)./stdY;
end
for t=1:length(subs);
sub=subs(t);
sub=cell2mat(sub);
Dummy=MRIread(['',sub,'/xhemi/surf/lh.thickness_z_on_lh.sm10.mgh']);
Dummy.vol(:)=0;
Dummy.vol(Cortex)=zMeasure_L(t,:);
% Change to patient directory
cd(subjects_dir)
MRIwrite(Dummy,['',sub,'/xhemi/surf/lh.Z_by_controls',Measures{L},''])
Dummy.vol(Cortex)=zMeasure_R(t,:);
MRIwrite(Dummy,['',sub,'/xhemi/surf/rh.Z_by_controls',Measures{L},''])
end
end