preclinical_MTI_PASL module

preclinical_MTI_PASL_pipeline

Calculates CBF with multi-TI preclinical PASL data. This function calculates CBF based on T1 relaxation differences between selective and global images.

preclinical_MTI_PASL_pipeline(
    data: np.ndarray,
    sel_index: list,
    glo_index: list,
    TI_list: list,
    mask_array=None,
    save_dir=None,
)

Parameters:

  • data (np.ndarray): The 3D image data array with dimensions corresponding to [height, width, number of selective and global images].

  • sel_index (list): Indices for selective images in the third dimension of the data array.

  • glo_index (list): Indices for global images in the third dimension of the data array.

  • TI_list (list): List of inversion times corresponding to sel_index and glo_index.

  • mask_array (np.ndarray, optional): A 2D binary mask array to isolate regions of interest in the calculation. Must match the first two dimensions of data.

  • save_dir (str, optional): Directory where the calculated CBF map and fitting curves are saved. If not provided, the CBF map is returned without saving.

Returns:

  • CBF (np.ndarray): The calculated CBF map.

Outputs:

  • If save_dir is provided, saves the CBF map as a NumPy array file (CBF.npy) and a figure illustrating the curve fitting (curvefit.png) in the specified directory.

Raises:

  • ValueError: If mask_array is not a NumPy array or its shape does not match the required dimensions.

T1fit_function

This function models T1 relaxation signal based on given parameters.

T1fit_function(xdata: np.ndarray, a: float, T1: float, A: float)

Parameters:

  • xdata (np.ndarray): An array of time points (usually TIs) at which the signal was measured.

  • a (float): Baseline offset of the signal.

  • T1 (float): T1 relaxation time.

  • A (float): Amplitude of the recovery signal.

Returns:

  • np.ndarray: An array representing the signal intensity calculated at each point in xdata using the given T1 model parameters.

T1fit

Performs non-linear curve fitting to derive T1 relaxation parameters from experimental data using the T1 relaxation model function.

T1fit(xdata: np.ndarray, ydata: np.ndarray)

Parameters:

  • xdata (np.ndarray): An array of time points (usually TIs) at which the MRI signal was measured.

  • ydata (np.ndarray): An array of signal intensities corresponding to each time point in xdata.

Returns:

  • A list containing the fitted parameters [a, T1, A], where:

    • a is the baseline offset of the signal.

    • T1 is the estimated T1 relaxation time.

    • A is the amplitude of the recovery signal.