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NMR_OPTIMA_BIDS/OPTIMA_convert_GE_BIDS_4.m
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| function OPTIMA_convert_GE_BIDS_4(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 15.10.2020 | |
| 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_%s_func_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3}); | |
| if ~test_flag system(cmd_str); end | |
| cmd_str = sprintf('date >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3}); | |
| if ~test_flag system(cmd_str); end | |
| cmd_str = sprintf('date >> %s/dwi/logfile_%s_%s_dwi_dcm2nii.txt',BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{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_%s_T1w -z y -o %s/anat %s >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, BIDS.output.dir, ... | |
| BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_T1w.dicom.1 >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| 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_%s_task-rest_run-1_bold -z y -o %s/func %s >> %s/func/logfile_%s_%s_func_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| filename = sprintf('%s/func/sub-%s_%s_task-rest_run-1_bold.json',BIDS.output.dir,BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| OPTIMA_dataset_func_description_BIDS_4(BIDS,filename, biomax_table{{'rest1'},:}); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_task-rest_run-1_bold.dicom.1 >> %s/func/logfile_%s_%s_func_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| system(cmd_str); | |
| cmd_str = sprintf('touch %s/func/sub-%s_%s_task-rest_run-1_bold_README.txt >> %s/func/logfile_%s_%s_func_dcm2nii.txt',... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| 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_%s_inplaneT2star_run-1 -z y -o %s/anat %s >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_inplaneT2star_run-1.dicom.1 >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| 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_%s_FLAIR -z y -o %s/anat %s >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_FLAIR.dicom.1 >> %s/anat/logfile_%s_%s_anat_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| system(cmd_str); | |
| end | |
| end | |
| end | |
| if logical(strfind(BIDS.input.data_dir(i).SeriesDescription{j},'fMRI SIT1')) | |
| if biomax_table{{'SIT1'},{'Ser'}} | |
| cmd_str = sprintf('dcm2niix -f sub-%s_%s_task-sit1_bold -z y -o %s/func %s >> %s/func/logfile_%s_%s_func_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| filename = sprintf('%s/func/sub-%s_%s_task-sit1_bold.json',BIDS.output.dir,BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| OPTIMA_dataset_func_description_BIDS_5(BIDS,filename, biomax_table{{'SIT1'},:}); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_task-sit1_bold.dicom.1 >> %s/func/logfile_%s_%s_func_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| system(cmd_str); | |
| cmd_str = sprintf('touch %s/func/sub-%s_%s_task-sit1_bold_README.txt >> %s/func/logfile_%s_%s_func_dcm2nii.txt',... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| 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_%s_run-1_dwi -z y -o %s/dwi %s >> %s/dwi/logfile_%s_%s_dwi_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_run-1_dwi.dicom.1 >> %s/dwi/logfile_%s_%s_dwi_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| system(cmd_str); | |
| end | |
| end | |
| end | |
| if logical(strfind(BIDS.input.data_dir(i).SeriesDescription{j},'polar')) | |
| if biomax_table{{'Pepolar'},{'Ser'}} | |
| % check number of dicom slices | |
| % and delete incomplete volumes | |
| tmp_str = sprintf('%s/i*MRDC*', BIDS.input.data_dir(i).subdir{j}); | |
| tmp = dir(tmp_str); | |
| n_images = size(tmp,1); | |
| full_images = fix(n_images/double(BIDS.input.data_dir(i).N_of_slices{j})); %adapt 60 | |
| for b = (full_images*BIDS.input.data_dir(i).N_of_slices{j})+1:n_images | |
| cmd_str = ['rm ', BIDS.input.data_dir(i).subdir{j},'/', tmp(b).name]; | |
| system(cmd_str); | |
| end | |
| cmd_str = sprintf('dcm2niix -f sub-%s_%s_run-2_dwi -z y -o %s/dwi %s >> %s/dwi/logfile_%s_%s_dwi_dcm2nii.txt',... | |
| BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| fprintf('\n%s', cmd_str); | |
| if ~test_flag | |
| system(cmd_str); | |
| cmd_str = sprintf('cp %s/*MRDC.1 %s/dicom/sub-%s_%s_run-2_dwi.dicom.1 >> %s/dwi/logfile_%s_%s_dwi_dcm2nii.txt', ... | |
| BIDS.input.data_dir(i).subdir{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}, ... | |
| BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{j}, BIDS.input.data_dir(1).GivenName{j}); | |
| system(cmd_str); | |
| end | |
| end | |
| end | |
| end | |
| end | |
| end | |
| cd([BIDS.input.dir]); |