A little function to get TR and slicetime order from dicoms

get_tr_and_sliceorder_from_dicoms.py

def get_tr_and_sliceorder(dicom_files, convention="SPM"):
    import numpy as np
    import dcmstack, dicom
    my_stack = dcmstack.DicomStack()
    for src_path in dicom_files:
        src_dcm = dicom.read_file(src_path)
        my_stack.add_dcm(src_dcm)
    nii_wrp = my_stack.to_nifti_wrapper()

    if convention == "french":
        sliceorder = np.argsort(np.argsort(nii_wrp.meta_ext.get_values('CsaImage.MosaicRefAcqTimes')[0])).tolist()
    elif convention == "SPM":
        sliceorder = np.argsort(nii_wrp.meta_ext.get_values('CsaImage.MosaicRefAcqTimes')[0]).tolist()

    tr = nii_wrp.meta_ext.get_values('RepetitionTime')
    return tr/1000.,sliceorder