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NMR_OPTIMA_BIDS/OPTIMA_convert_EDF_BIDS.m

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function OPTIMA_convert_EDF_BIDS(BIDS, biomax_table)
%
% copies the edf files into BIDS format
%
% Required fields of convert_EDF_BIDS:
%
% file history:
% created M. Czisch 31.1.2018
% last M. Czisch 28.3.2018
if logical(sum(biomax_table{:,{'EDF'}}))
fprintf('converting EDF files\n');
% create correct file name
short_ID = data_set_short_ID(BIDS);
cmd_str = sprintf('mkdir %s/physio', BIDS.output.dir); system(cmd_str);
cmd_str = sprintf('date >> %s/physio/logfile_%s_edf_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
cd([BIDS.input.dir]);
cd('EDF');
filenames = dir(['*', short_ID, '*.edf']);
max = size(filenames,1);
% loop over all possible log files
for i=1:max
clear cmd_str;
log_str = ['har', short_ID,'.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'faces'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-hariri_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['har', short_ID,'.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-hariri_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/har', short_ID,'.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/har', short_ID,'.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-hariri_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
log_str = ['Te', short_ID,'.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'TET'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-tet_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['Te', short_ID,'.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-tet_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/Te', short_ID,'.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/Te', short_ID,'.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-tet_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
log_str = ['N', short_ID,'.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'nback'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-nback_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['N', short_ID,'.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-nback_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/N', short_ID,'.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/N', short_ID,'.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-nback_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
log_str = ['Re', short_ID,'.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'Reward'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-reward_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['Re', short_ID,'.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-reward_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/Re', short_ID,'.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/Re', short_ID,'.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-reward_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
log_str = ['RS', short_ID,'.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'rest1'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['RS', short_ID,'.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
log_str = ['RS', short_ID,'b.edf'];
if strcmp(filenames(i).name,log_str) & biomax_table{{'rest2'},{'EDF'}}
cmd_str = sprintf('cp %s %s/physio/sub-%s_task-rest_run-2_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
log_str = ['RS', short_ID,'b.asc'];
if exist(log_str)
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-2_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'b.asc'])
log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'b.asc'];
cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-2_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str2);
else
cmd_str2 = sprintf('no asc file found');
end
end
if exist('cmd_str')
logfilename = sprintf('%s/physio/logfile_%s_edf_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fid = fopen(logfilename,'a');
fprintf(fid,'%s\n',cmd_str);
fclose(fid);
end
if exist('cmd_str2')
logfilename = sprintf('%s/physio/logfile_%s_edf_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fid = fopen(logfilename,'a');
fprintf(fid,'%s\n',cmd_str2);
fclose(fid);
end
end
end
cd([BIDS.input.dir]);