Skip to content
Permalink
master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?

NMR_OPTIMA_BIDS/OPTIMA_convert_GE_BIDS_3.m

Go to file
 
 
Cannot retrieve contributors at this time
154 lines (139 sloc) 9.28 KB
Raw Blame
Open in GitHub Desktop
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]);