diff --git a/brainiak/isc.py b/brainiak/isc.py index 99b9a69b4..df2e858f4 100644 --- a/brainiak/isc.py +++ b/brainiak/isc.py @@ -668,10 +668,9 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median', distribution of summary statistics. The p-value corresponds to either a 'two-sided', 'left'-, or 'right'-sided (default) test, as specified by side. According to Chen et al., 2016, this is the preferred nonparametric - approach for controlling false positive rates (FPR) for one-sample tests - in the pairwise approach. The efficacy of this approach for controlling - FPRs in the leave-one-out approach has not yet been systematically - evaluated. + approach for controlling false positive rates (FPRs) for one-sample tests + in the pairwise approach. Note that the bootstrap hypothesis test may not + strictly control FPRs in the leave-one-out approach. The implementation is based on the work in [Chen2016]_ and [HallWilson1991]_. @@ -714,8 +713,8 @@ def bootstrap_isc(iscs, pairwise=False, summary_statistic='median', p : float, p-value p-value based on bootstrap hypothesis test - distribution : ndarray, bootstraps by voxels (optional) - Bootstrap distribution if return_bootstrap=True + distribution : ndarray, n_bootstraps by voxels + Bootstrap distribution """ @@ -1088,8 +1087,8 @@ def permutation_isc(iscs, group_assignment=None, pairwise=False, # noqa: C901 The p-value corresponds to either a 'two-sided', 'left'-, or 'right'-sided (default) test, as specified by side. According to Chen et al., 2016, this is the preferred nonparametric approach for controlling false - positive rates (FPR) for two-sample tests. This approach may yield - inflated FPRs for one-sample tests. + positive rates (FPRs) for two-sample tests. Note that the permutation test + may not strictly control FPRs for one-sample tests. The implementation is based on the work in [Chen2016]_. @@ -1124,8 +1123,8 @@ def permutation_isc(iscs, group_assignment=None, pairwise=False, # noqa: C901 p : float, p-value p-value based on permutation test - distribution : ndarray, permutations by voxels (optional) - Permutation distribution if return_bootstrap=True + distribution : ndarray, n_permutations by voxels + Permutation distribution """ # Standardize structure of input data @@ -1281,7 +1280,8 @@ def timeshift_isc(data, pairwise=False, summary_statistic='median', False. Returns the observed ISC and p-values, as well as the null distribution of ISCs computed on randomly time-shifted data. The p-value corresponds to either a 'two-sided', 'left'-, or 'right'-sided (default) - test, as specified by side. + test, as specified by side. Note that circular time-shift randomization + may not strictly control false positive rates (FPRs). The implementation is based on the work in [Kauppi2010]_ and [Kauppi2014]_. @@ -1323,8 +1323,8 @@ def timeshift_isc(data, pairwise=False, summary_statistic='median', p : float, p-value p-value based on time-shifting randomization test - distribution : ndarray, time-shifts by voxels (optional) - Time-shifted null distribution if return_bootstrap=True + distribution : ndarray, n_shifts by voxels + Time-shifted null distribution """ # Check response time series input format @@ -1349,7 +1349,7 @@ def timeshift_isc(data, pairwise=False, summary_statistic='median', else: prng = np.random.RandomState(random_state) - # Get a random set of shifts based on number of TRs, + # Get a random set of shifts based on number of TRs shifts = prng.choice(np.arange(n_TRs), size=n_subjects, replace=True) @@ -1436,7 +1436,8 @@ def phaseshift_isc(data, pairwise=False, summary_statistic='median', to False. Returns the observed ISC and p-values, as well as the null distribution of ISCs computed on phase-randomized data. The p-value corresponds to either a 'two-sided', 'left'-, or 'right'-sided (default) - test, as specified by side. + test, as specified by side. Note that phase randomization may not + strictly control false positive rates (FPRs). The implementation is based on the work in [Lerner2011]_ and [Simony2016]_. @@ -1477,8 +1478,8 @@ def phaseshift_isc(data, pairwise=False, summary_statistic='median', p : float, p-value p-value based on time-shifting randomization test - distribution : ndarray, time-shifts by voxels (optional) - Time-shifted null distribution if return_bootstrap=True + distribution : ndarray, n_shifts by voxels + Phase-shifted null distribution """ # Check response time series input format