Register functional MRI images (fMRI) to template

transform_to_template.py

def transform_to_template(fn_func, fn_template, save=False):
    """
    Reads (4D)-functional images and transforms directly to template image
    Inputs: 
        - fn_func : Path to functional images
        - fn_template : Path to template brain, e.g. MNI template
        - save : Whether to save transformed image to same folder as functional
    Outputs:
        - func_template : functional images transformed to template brain
    """
    # Read functional images
    func = ants.image_read(fn_func)
    template = ants.image_read(fn_template)
    
    # Register mean functional image to template brain, use SyNBold as transform as we register directly on functional images
    anat_to_mni = ants.registration(fixed=template, moving=func.get_average_of_timeseries(),
                                    type_of_transform='SyNBold')
    
    # Now transform func to template space, use imagetype 3 for functional images
    func_template = ants.apply_transforms(fixed=template, moving=func, transformlist=anat_to_mni['fwdtransforms'],
                                          imagetype=3)
    
    # Save transformed functional image 
    if save_anat:
        fn_func_template = os.path.dirname(fn_func) + os.path.sep + 'template_' + os.path.basename(fn_func)
        ants.image_write(func_template, fn_func_template)
    return func_template