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test/convert_GE_BIDS.m

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function convert_GE_BIDS(BIDS, biomax_table)
%
% performes dicom2niix and saves data in BIDS format
%
% Required fields of convert_GE_BIDS:
%
% BIDS - BIDS structure
% biomax_table - biomax_out information in table format
%
%
% file history:
% created M. Czisch & F. Binder 20.11.2017
% last edited M. Czisch 31.1.2018
% flags are introduced to mark already processed files
flag_RSN2 = 0;
flag_RSN3 = 0;
for i = 1:2 % loop over days
max = size(BIDS.input.data_dir(i).ProtocolName,2);
if i == 1
cd([BIDS.input.dir,'/',BIDS.input.data_dir(1).name]);
for j = 3:max %ignore '.' and '..'
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'Sag FSPGR BRAVO 1x1x1mm')
if biomax_table{{'T1w'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_T1w -z y -o %s/anat %s >> %s/anat/logfile_anat_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI rest')
if biomax_table{{'rest1'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-rest_run-1_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'EPI segmentation T2w')
if biomax_table{{'EPI1'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_inplaneT2star_run-1 -z y -o %s/anat %s >> %s/anat/logfile_anat_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI TET')
if biomax_table{{'TET'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-tet_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'Ax T2 FLAIR')
if biomax_table{{'FLAIR'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_FLAIR -z y -o %s/anat %s >> %s/anat/logfile_anat_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI reward')
if biomax_table{{'Reward'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-reward_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'DTI 2.0 DSE 66 Dir Nex1')
if biomax_table{{'DTI'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_run-1_dwi -z y -o %s/dwi %s >> %s/dwi/logfile_dwi_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'DTI 2.0 DSE 66 Dir pepolar1')
if biomax_table{{'Pepolar'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_run-2_dwi -z y -o %s/dwi %s >> %s/dwi/logfile_dwi_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI n-back')
if biomax_table{{'nback'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-nback_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
end
elseif i==2
cd([BIDS.input.dir,'/',BIDS.input.data_dir(2).name]);
for j = 3:max %ignore '.' and '..'
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI faces')
if biomax_table{{'faces'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-hariri_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'EPI segmentation T2w')
if biomax_table{{'EPI2'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_inplaneT2star_run-2 -z y -o %s/anat %s >> %s/anat/logfile_anat_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI rest') & ~flag_RSN2
if biomax_table{{'rest2'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-rest_run-2_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
system(cmd_str);
flag_RSN2 = 1;
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI IST TR2000, 40SL')
if biomax_table{{'IST'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-ist_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
%system(cmd_str);
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI rest') & ~flag_RSN3
if biomax_table{{'rest3'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-rest_run-3_bold -z y -o %s/func %s >> %s/func/logfile_func_dcm2nii.txt',BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir);
fprintf('\n%s', cmd_str);
system(cmd_str);
flag_RSN3 = 1;
end
end
end
end
end
cd([BIDS.input.dir]);