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changed from bidscoin to dcm2niix + in-house sorting; set two_pass pr…
…ocessing as the default; documentation updates; updated tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,273 @@ | ||
| #!/usr/bin/env python3 | ||
| import argparse | ||
| import os | ||
| import sys | ||
| import subprocess | ||
| import glob | ||
| import json | ||
| import fnmatch | ||
|
|
||
| def load_json(path): | ||
| f = open(path) | ||
| j = json.load(f) | ||
| f.close() | ||
| return j | ||
|
|
||
| def rename(old, new, always_show=False): | ||
| if always_show or not sys.__stdin__.isatty(): | ||
| print(f'Renaming {old} -> {new}') | ||
| if not os.path.exists(os.path.split(new)[0]): | ||
| os.makedirs(os.path.split(new)[0], exist_ok=True) | ||
| os.rename(old, new) | ||
|
|
||
| def clean(data): | ||
| return data.replace('_', '') | ||
|
|
||
| def convert_to_nifti(input_dir, output_dir, t2starw_series_patterns, t1w_series_patterns, auto_yes): | ||
| print('Converting all DICOMs to nifti...') | ||
| subjects = os.listdir(input_dir) | ||
| for subject in subjects: | ||
| sessions = os.listdir(os.path.join(input_dir, subject)) | ||
| for session in sessions: | ||
| session_extra_folder = os.path.join(output_dir, clean(subject), session, "extra_data") | ||
| os.makedirs(session_extra_folder, exist_ok=True) | ||
| if 'dcm2niix_output.txt' in os.listdir(session_extra_folder): | ||
| print(f'Warning: {session_extra_folder} already has dcm2niix conversion output! Skipping...') | ||
| continue | ||
| series = os.listdir(os.path.join(input_dir, subject, session)) | ||
| for s in series: | ||
| series_dicom_folder = os.path.join(input_dir, subject, session, s) | ||
| print(f"dcm2niix -z n -o {session_extra_folder} {series_dicom_folder}") | ||
| subprocess.call(f"dcm2niix -z n -o {session_extra_folder} {series_dicom_folder} >> {os.path.join(session_extra_folder, 'dcm2niix_output.txt')}", executable='/bin/bash', shell=True) | ||
|
|
||
| print(f"Enumerating series names from JSON headers in '{output_dir}/.../extra_data' folders...") | ||
| all_series_names = [] | ||
| subjects = os.listdir(output_dir) | ||
| json_files = [] | ||
| json_datas = [] | ||
| for subject in subjects: | ||
| sessions = os.listdir(os.path.join(output_dir, subject)) | ||
| for session in sessions: | ||
| session_extra_folder = os.path.join(output_dir, subject, session, "extra_data") | ||
| json_files.extend(sorted(glob.glob(os.path.join(session_extra_folder, "*json")))) | ||
| json_datas.extend([load_json(json_file) for json_file in sorted(glob.glob(os.path.join(session_extra_folder, "*json")))]) | ||
| all_series_names = sorted(list(set([ | ||
| json_datas[i]['SeriesDescription'] | ||
| for i in range(len(json_datas)) | ||
| if json_datas[i]["Modality"] == "MR" | ||
| ]))) | ||
| if not all_series_names: | ||
| print(f"No valid series found in JSON headers in '{output_dir}/.../extra_data' folders!") | ||
| exit(1) | ||
| print(f"All series names identified: {all_series_names}") | ||
|
|
||
| # identify series using patterns | ||
| t2starw_series_names = [] | ||
| for t2starw_series_pattern in t2starw_series_patterns: | ||
| for series_name in all_series_names: | ||
| if fnmatch.fnmatch(series_name, t2starw_series_pattern): | ||
| t2starw_series_names.append(series_name) | ||
| t1w_series_names = [] | ||
| for t1w_series_pattern in t1w_series_patterns: | ||
| for series_name in all_series_names: | ||
| if fnmatch.fnmatch(series_name, t1w_series_pattern): | ||
| t1w_series_names.append(series_name) | ||
| if t2starw_series_names: | ||
| print(f"Chosen t2starw patterns {t2starw_series_patterns} matched with the following series: {t2starw_series_names}") | ||
| if t1w_series_names: | ||
| print(f"Chosen t1w patterns {t1w_series_patterns} matched with the following series: {t1w_series_names}") | ||
|
|
||
| if not t2starw_series_names and (sys.__stdin__.isatty() and not auto_yes): # if running interactively | ||
| print(f"No t2starw series found matching patterns: {t2starw_series_patterns}") | ||
| for i in range(len(all_series_names)): | ||
| print(f"{i+1}. {all_series_names[i]}") | ||
| while True: | ||
| user_input = input("Identify T2Starw scans for QSM (comma-separated numbers): ") | ||
| t2starw_scans_idx = user_input.split(",") | ||
| try: | ||
| t2starw_scans_idx = [int(j)-1 for j in t2starw_scans_idx] | ||
| except: | ||
| print("Invalid input") | ||
| continue | ||
| t2starw_scans_idx = sorted(list(set(t2starw_scans_idx))) | ||
| try: | ||
| t2starw_series_names = [all_series_names[j] for j in t2starw_scans_idx] | ||
| break | ||
| except: | ||
| print("Invalid input") | ||
| if t2starw_series_names: | ||
| print(f"Identified matching t2starw series: {t2starw_series_names}") | ||
| elif not t2starw_series_names: | ||
| print("Error: No t2starw series found!") | ||
| exit(1) | ||
|
|
||
| # identify T1w series | ||
| if not t1w_series_names and (sys.__stdin__.isatty() and not auto_yes): | ||
| print(f"No t1w series found matching pattern: {t1w_series_pattern}") | ||
| for i in range(len(all_series_names)): | ||
| print(f"{i+1}. {all_series_names[i]}") | ||
| while True: | ||
| user_input = input("Identify t1w scans for automated segmentation (comma-separated numbers; enter nothing to ignore): ").strip() | ||
| if user_input == "": | ||
| break | ||
| t1w_scans_idx = user_input.split(",") | ||
| try: | ||
| t1w_scans_idx = sorted(list(set([int(j)-1 for j in t1w_scans_idx]))) | ||
| except: | ||
| print("Invalid input") | ||
| continue | ||
| try: | ||
| t1w_series_names = [all_series_names[j] for j in t1w_scans_idx] | ||
| break | ||
| except: | ||
| print("Invalid input") | ||
| if t1w_series_names: | ||
| print(f"Identified matching t1w series: {t1w_series_names}") | ||
| if not t1w_series_names: | ||
| print(f"Warning: No t1w series found matching patterns {t1w_series_patterns}! Automated segmentation will not be possible.") | ||
|
|
||
| print('Parsing JSON headers...') | ||
| all_session_details = [] | ||
| for subject in subjects: | ||
| sessions = os.listdir(os.path.join(output_dir, subject)) | ||
| for session in sessions: | ||
| session_extra_folder = os.path.join(output_dir, subject, session, "extra_data") | ||
| session_anat_folder = os.path.join(output_dir, subject, session, "anat") | ||
| json_files = sorted(glob.glob(os.path.join(session_extra_folder, "*json"))) | ||
| session_details = [] | ||
| for json_file in json_files: | ||
| json_data = load_json(json_file) | ||
| if json_data['Modality'] == 'MR' and json_data['SeriesDescription'] in t2starw_series_names + t1w_series_names: | ||
| details = {} | ||
| details['subject'] = subject | ||
| details['session'] = session | ||
| details['series_type'] = None | ||
| if json_data['SeriesDescription'] in t2starw_series_names: | ||
| details['series_type'] = 't2starw' | ||
| elif json_data['SeriesDescription'] in t1w_series_names: | ||
| details['series_type'] = 't1w' | ||
| details['series_num'] = json_data['SeriesNumber'] | ||
| details['part_type'] = 'phase' if 'P' in json_data['ImageType'] else 'magnitude' | ||
| details['echo_time'] = json_data['EchoTime'] | ||
| details['file_name'] = json_file.split('.')[0] | ||
| details['run_num'] = None | ||
| details['echo_num'] = None | ||
| details['num_echoes'] = None | ||
| details['new_name'] = None | ||
| session_details.append(details) | ||
| session_details = sorted(session_details, key=lambda f: (f['subject'], f['session'], f['series_type'], f['series_num'], 0 if 'phase' in f['part_type'] else 1, f['echo_time'])) | ||
|
|
||
| # update run numbers | ||
| run_num = 1 | ||
| series_num = session_details[0]['series_num'] | ||
| series_type = session_details[0]['series_type'] | ||
| for i in range(len(session_details)): | ||
| if session_details[i]['series_num'] != series_num: | ||
| if session_details[i]['series_type'] == 't2starw' and session_details[i-1]['part_type'] == 'phase': | ||
| run_num += 1 | ||
| elif session_details[i]['series_type'] == 't1w' and session_details[i-1]['series_type'] == 't1w': | ||
| run_num += 1 | ||
| elif session_details[i]['series_type'] != session_details[i-1]['series_type']: | ||
| run_num = 1 | ||
|
|
||
| series_num = session_details[i]['series_num'] | ||
| series_type = session_details[0]['series_type'] | ||
| session_details[i]['run_num'] = run_num | ||
|
|
||
| # update echo numbers and number of echoes | ||
| t2starw_details = [details for details in session_details if details['series_type'] == 't2starw'] | ||
| t2starw_run_nums = sorted(list(set(details['run_num'] for details in t2starw_details))) | ||
| for run_num in t2starw_run_nums: | ||
| echo_times = sorted(list(set([details['echo_time'] for details in t2starw_details if details['run_num'] == run_num]))) | ||
| num_echoes = len(echo_times) | ||
| for details in t2starw_details: | ||
| if details['run_num'] == run_num: | ||
| details['num_echoes'] = num_echoes | ||
| details['echo_num'] = echo_times.index(details['echo_time']) + 1 | ||
|
|
||
| # update names | ||
| for details in session_details: | ||
| if details['series_type'] == 't1w': | ||
| details['new_name'] = os.path.join(session_anat_folder, f"{clean(subject)}_{clean(session)}_run-{details['run_num']}_T1w") | ||
| elif details['num_echoes'] == 1: | ||
| details['new_name'] = os.path.join(session_anat_folder, f"{clean(subject)}_{clean(session)}_run-{details['run_num']}_part-{details['part_type']}_T2starw") | ||
| else: | ||
| details['new_name'] = os.path.join(session_anat_folder, f"{clean(subject)}_{clean(session)}_run-{details['run_num']}_echo-{details['echo_num']}_part-{details['part_type']}_MEGRE") | ||
|
|
||
| # store session details | ||
| all_session_details.extend(session_details) | ||
|
|
||
| # if running interactively, show a summary of the renames prior to actioning | ||
| if sys.__stdin__.isatty() and not auto_yes: | ||
| print("Summary of identified files and proposed renames (following BIDS standard):") | ||
| for f in all_session_details: | ||
| print(f"{os.path.split(f['file_name'])[1]} \n\t -> {os.path.split(f['new_name'])[1]}") | ||
| if input("Confirm renaming? (n for no): ").strip().lower() in ["n", "no"]: | ||
| exit() | ||
|
|
||
| # rename all files | ||
| print("Renaming files...") | ||
| for details in all_session_details: | ||
| rename(details['file_name']+'.json', details['new_name']+'.json', always_show=auto_yes) | ||
| rename(details['file_name']+'.nii', details['new_name']+'.nii', always_show=auto_yes) | ||
| print("Finished!") | ||
|
|
||
| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser( | ||
| description="QSMxT dicomConvert: Converts DICOM files to NIfTI/BIDS", | ||
| formatter_class=argparse.ArgumentDefaultsHelpFormatter | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| 'input_dir', | ||
| help='Sorted DICOM directory generated using run_0_dicomSort.py of the format {subject}/{session}/{series}' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| 'output_dir', | ||
| help='Output directory for converted NIfTIs' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| '--use_patient_names', | ||
| action='store_true', | ||
| help='Use the PatientName rather than PatientID for subject folders' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| '--use_session_dates', | ||
| action='store_true', | ||
| help='Use the StudyDate field rather than an incrementer for session IDs' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| '--auto_yes', | ||
| action='store_true', | ||
| help='Force running non-interactively' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| '--t2starw_series_patterns', | ||
| default=['*t2starw*'], | ||
| nargs='*', | ||
| help='Patterns used to identify t2starw series for QSM from the DICOM SeriesDescription field' | ||
| ) | ||
|
|
||
| parser.add_argument( | ||
| '--t1w_series_patterns', | ||
| default=['*t1w*'], | ||
| nargs='*', | ||
| help='Patterns used to identify t1w series for segmentation from the DICOM SeriesDescription field' | ||
| ) | ||
|
|
||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| convert_to_nifti( | ||
| input_dir=args.input_dir, | ||
| output_dir=args.output_dir, | ||
| t2starw_series_patterns=args.t2starw_series_patterns, | ||
| t1w_series_patterns=args.t1w_series_patterns, | ||
| auto_yes=args.auto_yes | ||
| ) | ||
|
|
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