Additionnal utility functions
Get a list of patient by types
If no types are provided, print a list of patients for each type present in the study. If a specific type is provided, only print the list of patient corresponding to that type.
elikopy.utils.get_patient_list_by_types(folder_path, type=None)
Merge all global reports
Merge all subjects quality control reports into a single report.
elikopy.utils.merge_all_reports(folder_path)
Dicom to NifTi
Convert DICOM data into compressed NIFTIs. Converted DICOMs are then moved to a sub-folder named original_data. The NIFTIs are named patientID_ProtocolName_SequenceName.
elikopy.core.dicom_to_nifti(folder_path)
Anonymise NifTi
Anonymize all NIFTIs present in rootdir by removing the PatientName and PatientBirthDate (only month and day) in the json and renaming the NIFTI files name to the PatientID.
rootdir - Folder containing all the nifti to anonimyse.
anonymize_json - If true, edit the json to remove the PatientName and replace the PatientBirthDate by the year of birth.
rename - If true, rename the nifti to the PatientID.
elikopy.core.anonymise_nifti(rootdir,anonymize_json,rename)