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NMR_OPTIMA_BIDS/OPTIMA_convert_GE_BIDS_3.m

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function OPTIMA_convert_GE_BIDS_3(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
% adapted to inclue SIT1 M. Czisch 17.7.2019
% last edited M. Czisch 05.11.2019
test_flag = 0; % if test then 1
% flags are introduced to mark already processed files
flag_RSN2 = 0;
flag_RSN3 = 0;
fprintf('converting GE files\n');
cmd_str = sprintf('date >> %s/func/logfile_%s_func_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
if ~test_flag system(cmd_str); end
cmd_str = sprintf('date >> %s/anat/logfile_%s_anat_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
if ~test_flag system(cmd_str); end
cmd_str = sprintf('date >> %s/dwi/logfile_%s_dwi_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
if ~test_flag system(cmd_str); end
cmd_str = sprintf('mkdir %s/dicom',BIDS.output.dir); system(cmd_str);
number_of_days = size(BIDS.input.data_dir,2);
for i = 1:number_of_days % loop over days
max = size(BIDS.input.data_dir(i).subdir,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_%s_anat_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_T1w.dicom.1 >> %s/anat/logfile_%s_anat_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
end
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_%s_func_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
filename = sprintf('%s/func/sub-%s_task-rest_run-1_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
OPTIMA_dataset_func_description_BIDS_3(BIDS,filename, biomax_table{{'rest1'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-rest_run-1_bold.dicom.1 >> %s/func/logfile_%s_func_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
cmd_str = sprintf('touch %s/func/sub-%s_task-rest_run-1_bold_README.txt >> %s/func/logfile_%s_func_dcm2nii.txt',...
BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
system(cmd_str);
end;
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_%s_anat_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_inplaneT2star_run-1.dicom.1 >> %s/anat/logfile_%s_anat_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
end;
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_%s_anat_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_FLAIR.dicom.1 >> %s/anat/logfile_%s_anat_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
end;
end
end
if strcmp(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI SIT1')
if biomax_table{{'SIT1'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_task-sit1_bold -z y -o %s/func %s >> %s/func/logfile_%s_func_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
filename = sprintf('%s/func/sub-%s_task-sit1_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
OPTIMA_dataset_func_description_BIDS_3(BIDS,filename, biomax_table{{'SIT1'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-sit1_bold.dicom.1 >> %s/func/logfile_%s_func_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
cmd_str = sprintf('touch %s/func/sub-%s_task-sit1_bold_README.txt >> %s/func/logfile_%s_func_dcm2nii.txt',...
BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
system(cmd_str);
end;
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_%s_dwi_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_run-1_dwi.dicom.1 >> %s/dwi/logfile_%s_dwi_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
end;
end
end
if logical(strfind(BIDS.input.data_dir(i).SeriesDescription{j},'polar'))
if biomax_table{{'Pepolar'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_run-2_dwi -z y -o %s/dwi %s >> %s/dwi/logfile_%s_dwi_dcm2nii.txt',...
BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
fprintf('\n%s', cmd_str);
if ~test_flag
system(cmd_str);
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_run-2_dwi.dicom.1 >> %s/dwi/logfile_%s_dwi_dcm2nii.txt', ...
BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(i).PatientID{j}, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
system(cmd_str);
end;
end
end
end
end
end
cd([BIDS.input.dir]);