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NMR_OPTIMA_BIDS/OPTIMA_convert_GE_BIDS.m

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function OPTIMA_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 27.3.2018
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});
dataset_func_description_BIDS(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},'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_%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-tet_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'TET'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-tet_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-tet_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},'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 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_%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-reward_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'Reward'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-reward_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-reward_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
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_%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-nback_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'nback'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-nback_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-nback_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
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'}}
%check_slice_order(BIDS.input.data_dir(i).subdir{j});
cmd_str = sprintf('dcm2niix -f sub-%s_task-hariri_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-hariri_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'faces'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-hariri_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-hariri_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{{'EPI2'},{'Ser'}}
cmd_str = sprintf('dcm2niix -f sub-%s_inplaneT2star_run-2 -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-2.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') & ~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_%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-2_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'rest2'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-rest_run-2_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-2_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;
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_%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-ist_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'IST'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-ist_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-ist_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},'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_%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-3_bold.json',BIDS.output.dir,BIDS.input.data_dir(i).PatientID{j});
dataset_func_description_BIDS(BIDS,filename, biomax_table{{'rest3'},:});
cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_task-rest_run-3_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-3_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;
flag_RSN3 = 1;
end
end
end
end
end
cd([BIDS.input.dir]);