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make_std_env.m
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make_std_env.m
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function make_std_env(handles)
%% Internal variables
fs=filesep;
env_folder=[handles.env.path_gagui fs ...,
handles.env.name{1} fs,...
handles.func_data_name fs,...
handles.env.group];
if ~isfolder(env_folder)
mkdir(env_folder);
end
change_permissions(handles,env_folder)
n_parcel=length(handles.mc.surv_parcels);
% Identify participants surviving motion censoring
surv=handles.mc.surv_ix;
% surv(:,1)=[]; %first column refers to standard, second one to model based
surv(:,2)=[]; %first column refers to standard, second one to model based
n_surv=sum(surv);
ix=find(surv);
n_frames = floor(handles.mc.min_frames);% identify the min frames set in th
n_surv_frames=handles.mc.n_surv_frames;
n_surv_frames=n_surv_frames(ix,:);
n_frames2= min(n_surv_frames);% identify the min number of frames after censoring (this number must be equal or larger that the previous one)
n_frames2(2:end)=[];
%% read mask
mask=cell(n_surv,3);
for i=1:n_surv
mask{i,1}=handles.mc.surv_std{ix(i)};
% get indices of remaining frames and randomly select n numder of
% remaining frames where n is the minimum number of frames after
% censoring
mask{i,2}=zeros(length(handles.mc.surv_std{ix(i)}),1);
if sum(handles.mc.surv_std{ix(i)}) >= n_frames2
inc_frames_idx=find(handles.mc.surv_std{ix(i)}==1);
sample_inc_frames_idx=datasample(inc_frames_idx, n_frames2,'Replace',false);
mask{i,2}(sample_inc_frames_idx)=1;
end
mask{i,3}=zeros(length(handles.mc.surv_std{ix(i)}),1);
if sum(handles.mc.surv_std{ix(i)}) >= n_frames
inc_frames_idx=find(handles.mc.surv_std{ix(i)}==1);
sample_inc_frames_idx=datasample(inc_frames_idx, n_frames,'Replace',false);
mask{i,3}(sample_inc_frames_idx)=1;
end
end
mask_file=[env_folder fs handles.env.std_mask_name];
save_planB(mask_file,mask);%n_frames
%% Read parcellated data
for i=1:n_parcel
% Identify parcel and preallocate memory
j=strcmp(cat(1,{handles.cbh.String}'),strtrim(char(handles.mc.surv_parcels{i})));
if handles.cbh(find(j)).Value
parcel_folder=[env_folder fs strtrim(char(handles.mc.surv_parcels{i}))];
if ~isfolder(parcel_folder)
mkdir(parcel_folder)
end
change_permissions(handles,parcel_folder)
if handles.save_raw_timecourses_flag
raw_tc=cell(n_surv,1);
end
% masked_tc=cell(n_surv,1);
handles.mc.min_frames;
% read the first participant to preallocate memory for fconn
j=1;
disp(['Processing participant ' num2str(j) ' out of ' num2str(n_surv) ' in parcel ' handles.mc.surv_parcels{i} ' (' num2str(i) ' out of ' num2str(n_parcel) '), standard']);
path_to_nii=[strtrim(handles.participants.full_path(ix(j),:)) fs 'func'];
%path_to_csv=[strtrim(handles.participants.full_path(ix(j),:)) fs handles.paths.append_path_csv_parcellations];
% filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '_task-rest_bold_atlas-' handles.mc.surv_parcels{i} '.nii'],'');
%filename=[handles.mc.surv_parcels{n_parcel} '.csv'];
% temp_raw=ciftiopen([path_to_nii fs filename], '/home/exacloud/lustre1/fnl_lab/code/external/utilities/workbench-1.2.3-HCP/bin_rh_linux64/wb_command');% read raw timecourses
% temp_raw=ciftiopen([path_to_nii fs filename], handles.paths.wb_command);% read raw timecourses
try
filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '*-rest*bold_atlas-' handles.mc.surv_parcels{i} '.nii'],'');
local_filename=strtrim(ls([path_to_nii fs filename]));
catch
filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '*-rest*bold*-' handles.mc.surv_parcels{i} '.nii'],'');
local_filename=strtrim(ls([path_to_nii fs filename]));
end
TEMP_RAW = read_cifti_via_csv (local_filename,quotes_if_space(handles.paths.wb_command));
% OUTLIER DETECTION - Anders Perrone 20180516
%stdev=std(temp_raw,0,2);
%FDvec_keep_idx=find(mask{j}==1);
%Outlier_file=isthisanoutlier(stdev(FDvec_keep_idx),'median');
%Outlier_idx=find(Outlier_file==1); % find outlier indices
%mask{j}(FDvec_keep_idx(Outlier_idx))=0; % set outliers to zero within FDvec
%handles.mc.n_surv_frames(ix(j),1)=handles.mc.n_surv_frames(ix(j),1)-length(Outlier_idx)
%n_frames2=min(handles.mc.n_surv_frames(ix(j),1))
% temp_raw_masked=temp_raw.cdata(:,mask{j,1});% mask raw timecourses
% raw_tc{j}=temp_raw.cdata;
% masked_tc{j}=temp_raw_masked;
temp_raw_masked=TEMP_RAW(:,mask{j,1});% mask raw timecourses
if handles.save_raw_timecourses_flag
raw_tc{j}=TEMP_RAW;
end
% masked_tc{j}=temp_raw_masked;
% n_rois=size(temp_raw.cdata,1);
n_rois=size(TEMP_RAW,1);
fconn_temp=zeros(n_rois,n_rois,n_surv,3);
%if i==6
% 1;
%end
%ix1=randperm(handles.mc.n_surv_frames(ix(j),1),n_frames);
%ix1=find(mask{j,3}==1);
% fconn_temp(:,:,j,1)=corr(temp_raw.cdata(:,mask{j,3}==1).');
fconn_temp(:,:,j,1)=corr(TEMP_RAW(:,mask{j,3}==1).');
%ix2=randperm(handles.mc.n_surv_frames(ix(j),1),n_frames2);
%ix2=find(mask{j,2}==1);
% fconn_temp(:,:,j,2)=corr(temp_raw.cdata(:,mask{j,2}==1).');
fconn_temp(:,:,j,2)=corr(TEMP_RAW(:,mask{j,2}==1)');
% fconn_temp(:,:,j,3)=corr(temp_raw.cdata(:,mask{j,1}==1).');
fconn_temp(:,:,j,3)=corr(TEMP_RAW(:,mask{j,1}==1)');
for j=2:n_surv
disp(['Processing participant ' num2str(j) ' out of ' num2str(n_surv) ' in parcel ' handles.mc.surv_parcels{i} ' (' num2str(i) ' out of ' num2str(n_parcel) '), standard']);
path_to_nii=[strtrim(handles.participants.full_path(ix(j),:)) fs 'func'];
% filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '_task-rest_bold_atlas-' handles.mc.surv_parcels{i} '.nii'],'');
filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '*-rest*bold_atlas-' handles.mc.surv_parcels{i} '.nii'],'');
try
filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '*-rest*bold_atlas-' handles.mc.surv_parcels{i} '.nii'],'');
local_filename=strtrim(ls([path_to_nii fs filename]));
catch
filename=strjoin([handles.participants.ids(ix(j),:) '_' handles.participants.visit_folder(ix(j),:) '*-rest*bold*-' handles.mc.surv_parcels{i} '.nii'],'');
local_filename=strtrim(ls([path_to_nii fs filename]));
end
%filename=[handles.mc.surv_parcels{n_parcel} '.csv'];
% temp_raw=ciftiopen([path_to_nii fs filename], '/home/exacloud/lustre1/fnl_lab/code/external/utilities/workbench-1.2.3-HCP/bin_rh_linux64/wb_command');
% temp_raw=ciftiopen([path_to_nii fs filename], handles.paths.wb_command);
TEMP_RAW=read_cifti_via_csv (local_filename,quotes_if_space(handles.paths.wb_command));
% OUTLIER DETECTION - Anders Perrone 20180516
%stdev=std(temp_raw,0,2);
%FDvec_keep_idx=find(mask{j}==1);
%Outlier_file=isthisanoutlier(stdev(FDvec_keep_idx),'median');
%Outlier_idx=find(Outlier_file==1); % find outlier indices
%mask{j}(FDvec_keep_idx(Outlier_idx))=0; % set outliers to zero within FDvec
%handles.mc.n_surv_frames(ix(j),1)=handles.mc.n_surv_frames(ix(j),1)-length(Outlier_idx)
%n_frames2=min(handles.mc.n_surv_frames(ix(j),1))
% temp_raw_masked=temp_raw.cdata(:,mask{j,1});
% raw_tc{j}=temp_raw.cdata;
% masked_tc{j}=temp_raw_masked;
temp_raw_masked=TEMP_RAW(:,mask{j,1});
if handles.save_raw_timecourses_flag
raw_tc{j}=TEMP_RAW;
end
% masked_tc{j}=temp_raw_masked;
%ix1=randperm(handles.mc.n_surv_frames(ix(j),1),n_frames);
%ix1=find(mask{j,3}==1);
% fconn_temp(:,:,j,1)=corr(temp_raw.cdata(:,mask{j,3}==1).');
fconn_temp(:,:,j,1)=corr(TEMP_RAW(:,mask{j,3}==1).');
%ix2=randperm(handles.mc.n_surv_frames(ix(j),1),n_frames2);
%ix2=find(mask{j,2}==1);
% fconn_temp(:,:,j,2)=corr(temp_raw.cdata(:,mask{j,2}==1).');
fconn_temp(:,:,j,2)=corr(TEMP_RAW(:,mask{j,2}==1).');
% fconn_temp(:,:,j,3)=corr(temp_raw.cdata(:,mask{j,1}==1).');
fconn_temp(:,:,j,3)=corr(TEMP_RAW(:,mask{j,1}==1).');
end
disp(['Saving data from parcel ' handles.mc.surv_parcels{i} ' (' num2str(i) ' out of ' num2str(n_parcel) ')']);
if handles.save_raw_timecourses_flag
save_planB([parcel_folder fs handles.env.raw_tc],raw_tc);
% save_planB([parcel_folder fs handles.env.masked_tc],masked_tc);
end
fconn=squeeze(fconn_temp(:,:,:,1));
file_fconn=['fconn_' num2str(n_frames) '_frames.mat'];
save_planB([parcel_folder fs file_fconn],fconn);
fconn=squeeze(fconn_temp(:,:,:,2));
file_fconn=['fconn_' num2str(n_frames2) '_frames.mat'];
save_planB([parcel_folder fs file_fconn],fconn);
fconn=squeeze(fconn_temp(:,:,:,3));
file_fconn='fconn_all_surv_frames.mat';
save_planB([parcel_folder fs file_fconn],fconn);
%% patch added in Oct 10, 2016 by Oscar Miranda to add Fisher Z transform
% Zfconn_temp=atanh(fconn_temp);
%
% fconn=squeeze(Zfconn_temp(:,:,:,1));
% file_fconn=['Zfconn_' num2str(n_frames) '_frames.mat'];
% save_planB([parcel_folder fs file_fconn],fconn);
%
% fconn=squeeze(Zfconn_temp(:,:,:,2));
% file_fconn=['Zfconn_' num2str(n_frames2) '_frames.mat'];
% save_planB([parcel_folder fs file_fconn],fconn);
%
% fconn=squeeze(Zfconn_temp(:,:,:,3));
% file_fconn='Zfconn_all_surv_frames.mat';
% save_planB([parcel_folder fs file_fconn],fconn);
end
end