Module poldracklab.fmri

Provide functions for working with fMRI data

This module provides functions for working with fMRI data, including generating hemodynamic response functions (HRFs).

The module contains the following functions:

• spm_hrf(): Generates a hemodynamic response function (HRF) using a combination of two gamma functions.

Functions

def spm_hrf(TR: (, ),
fMRI_T: float = 16.0,
p: numpy.ndarray | None = None) ‑> numpy.ndarray

Expand source code

def spm_hrf(
    TR: (float, np.ndarray), fMRI_T: float = 16.0, p: Optional[np.ndarray] = None
) -> np.ndarray:
    """An implementation of spm_hrf.m from the SPM distribution: Generates a hemodynamic response function (HRF)
    using a combination of two gamma functions.

    Args:

        TR: repetition time(s) at which to generate the HRF (in seconds)

        fMRI_T: time steps per second for the hrf (default 16)

        p: list with parameters of the two gamma functions:

            p[0] - delay of response (relative to onset)         6
            p[1] - delay of undershoot (relative to onset)      16
            p[2] - dispersion of response                        1
            p[3] - dispersion of undershoot                      1
            p[4] - ratio of response to undershoot               6
            p[5] - onset (seconds)                               0
            p[6] - length of kernel (seconds)                   32

    Returns:
        np.ndarray: HRF(s)
    """

    if p is None:
        p = np.array([6, 16, 1, 1, 6, 0, 32])

    TR = float(TR)
    dt = TR / fMRI_T
    u = np.arange(p[6] / dt + 1) - p[5] / dt
    hrf = (
        scipy.stats.gamma.pdf(u, p[0] / p[2], scale=1.0 / (dt / p[2]))
        - scipy.stats.gamma.pdf(u, p[1] / p[3], scale=1.0 / (dt / p[3])) / p[4]
    )
    good_pts = np.array(range(int(p[6] / TR))) * fMRI_T
    hrf = hrf[list(good_pts.astype("int"))]
    # hrf = hrf([0:(p(7)/RT)]*fMRI_T + 1);
    hrf = hrf / np.sum(hrf)
    return hrf

An implementation of spm_hrf.m from the SPM distribution: Generates a hemodynamic response function (HRF) using a combination of two gamma functions.

Args

TR

repetition time(s) at which to generate the HRF (in seconds)

fMRI_T

time steps per second for the hrf (default 16)

p

list with parameters of the two gamma functions:

p[0] - delay of response (relative to onset) 6 p[1] - delay of undershoot (relative to onset) 16 p[2] - dispersion of response 1 p[3] - dispersion of undershoot 1 p[4] - ratio of response to undershoot 6 p[5] - onset (seconds) 0 p[6] - length of kernel (seconds) 32

Returns

np.ndarray

HRF(s)